title: DM1_F?_D_03

description: DM1 patient, age unknown, gender Female

tag: bipsy site


title: Adult worms treated Tris 10nM pH 8,8 (vehicle) during 1h rep 3 (Control sample 3) cy3

status: Public on Dec 15 2009

type: RNA

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

description: No additional information

hyb_protocol: The hybridization solution and procedure were prepared according to manufacturer´s instructions.

scan_protocol: Slides were air dried and scanned using a microarray dual channel laser scanner (GenePix 4000B, Molecular Devices, USA) 100 % laser power and PMT levels were adjusted in order to obtain similar average intensities of red and green signal.

data_processing: Data was extracted from images using the Feature Extraction software (Agilent Technologies). Spots with low intensities were filtered out according to criteria established by Feature Extraction software (IsPosAndSig collun). Normalization was perfomed using the Quantiles algorithm.

molecule: total RNA

organism: Schistosoma mansoni

source_name: Adult worms

label_protocol: Three hundred nanograms of total RNA from each sample were amplified using the Linear RNA amplification and labeling kit (Agilent Technologies) according to manufacturer´s instructions. Eight hundred and twenty five nanograms Cy3 labeled cRNA was used to hibridization.

extract_protocol: Total RNA was obtained using Trizol reagent (Invitrogen) according to the manufacturer's instructions. The RNA was quantified using the Nanodrop ND-1000 UV/Vis spectrophotometer and RNA integrity was checked by electrophoresis with an Agilent 2100 Bioanalyzer. Total RNA was treated with DNAse I (QIAGEN) and subsequently purified using RNA easy mini kit

tag: stage

value: adult worms recovered forty-two days after infection of hamster


title: 3 hour old early-schistosomula treated with human TNF-alpha bio rep 2 tech rep 2 cy3

description: No additional information

source_name: 3 hour old early-schistosomula

treatment_protocol: The Schistosoma mansoni just 3 h after cercariae-to-schistosomula in vitro transformation were incubated in vitro (37 oC, 5% CO2 ) with Tris-HCL (10nM) pH 8,8 during 1h.

value: cercariae-to-schistosomula


title: Adult worms treated with human TNF-alpha during 24hs rep 3 cy3

description: No additional information


title: 3 hour old early-schistosomula treated with human TNF-alpha bio rep 2 tech rep 2 cy5

description: No additional information

label_protocol: Three hundred nanograms of total RNA from each sample were amplified using the Linear RNA amplification and labeling kit (Agilent Technologies) according to manufacturer´s instructions. Eight hundred and twenty five nanograms Cy5 labeled cRNA was used to hibridization.


title: 3 hour old early-schistosomula treated with human TNF-alpha bio rep 1 tech rep 2 cy5

description: No additional information


title: 3 hour old early-schistosomula treated with human TNF-alpha bio rep 2 tech rep 1 cy3

description: No additional information


title: Adult worms treated with human TNF-alpha during 1h rep 3 cy3

description: No additional information


title: 3 hour old early-schistosomula treated with human TNF-alpha bio rep 2 tech rep 1 cy5

description: No additional information


title: 3 hour old early-schistosomula treated with Tris-HCL (10nM) pH8,8 during 1h (control) rep 3 cy5

description: No additional information


title: Adult worms treated Tris 10nM pH 8,8 (vehicle) during 1h rep 3 (Control sample 3) cy5

description: No additional information


title: 3 hour old early-schistosomula treated with human TNF-alpha bio rep 1 tech rep 1 cy3

description: No additional information


title: 3 hour old early-schistosomula treated with human TNF-alpha bio rep 1 tech rep 1 cy5

description: No additional information


title: Adult worms treated Tris 10nM pH 8,8 (vehicle) during 1h rep 2 (Control sample 2) cy3

description: No additional information

treatment_protocol: The Schistosoma mansoni adult paired worms were recovered forty two days after infection of hamster. The worms were incubated in vitro (37 oC, 5% CO2) with Tris (10nM) pH8,8 during 1h.


title: Adult worms treated with human TNF-alpha during 1h rep 2 cy3

description: No additional information

treatment_protocol: The Schistosoma mansoni adult paired worms were recovered forty two days after infection of hamster. The worms were incubated in vitro (37 oC, 5% CO2) with human TNF-alpha (20nM) during 1h.


title: Adult worms treated with human TNF-alpha during 1h rep 3 cy5

description: No additional information


title: Adult worms treated Tris 10nM pH 8,8 (vehicle) during 24hs rep 1 (Control sample 1) cy3

description: No additional information

treatment_protocol: The Schistosoma mansoni adult paired worms were recovered forty two days after infection of hamster. The worms were incubated in vitro (37 oC, 5% CO2) with Tris (10nM) pH8,8 during 24hs.


title: Adult worms treated Tris 10nM pH 8,8 (vehicle) during 1h rep 1 (Control sample 1) cy3

description: No additional information


title: Adult worms treated Tris 10nM pH 8,8 (vehicle) during 24hs rep 2 (Control sample 2) cy5

description: No additional information


title: Adult worms treated with human TNF-alpha during 1h rep 1 cy5

description: No additional information


title: Adult worms treated with human TNF-alpha during 1h rep 2 cy5

description: No additional information


title: Adult worms treated with human TNF-alpha during 24hs rep 1 cy5

description: No additional information

treatment_protocol: The Schistosoma mansoni adult paired worms were recovered forty two days after infection of hamster. The worms were incubated in vitro (37 oC, 5% CO2) with human TNF-alpha (20nM) during 24hs.


title: Adult worms treated Tris 10nM pH 8,8 (vehicle) during 1h rep 1 (Control sample 1) cy5

description: No additional information


title: Adult worms treated with human TNF-alpha during 24hs rep 1 cy3

description: No additional information


title: Adult worms treated with human TNF-alpha during 1h rep 1 cy3

description: No additional information


title: Adult worms treated Tris 10nM pH 8,8 (vehicle) during 24hs rep 2 (Control sample 2) cy3

description: No additional information


title: 3 hour old early-schistosomula treated with human TNF-alpha bio rep 1 tech rep 2 cy3

description: No additional information


title: Adult worms treated with human TNF-alpha during 24hs rep 2 cy3

description: No additional information


title: Caruncular_Pregnant_9790_Sub-fertile

status: Public on Dec 01 2009

city: Auckland

first: Caroline

middle: Gwendolyn

last: Walker

state: Outside the US or Canada

address: 3A symonds st

department: University of Auckland

country: New Zealand

institute: DairyNZ Ltd

hyb_protocol: 825ng of both Cy3 and Cy5 labelled aRNA was used for microarray hybridisation using the Agilent Gene Expression Hybridisation Kit (60-mer oligo microarray protocol version 4.0) (Agilent Technologies, Bioresearch Solutions Unit, 3500 Deer Creek Road, Palo Alto, CA 94034, USA).  Dye-labelled, fragmented aRNA was then added to each Agilent 44k 60-mer oligonucleotide microarray, hybridised over night (17 hours), washed and allowed to air dry.

scan_protocol: Arrays were then scanned using the Agilent DNA microarray scanner.

data_processing: Agilent feature extraction software version 7.1 was used to analyse the scanned Agilent microarray. The 44 scanned microarray image files were uploaded to the feature extraction software. Using the design file (015354) the feature extraction software locates features and converts the extracted data from each feature into a quantitative log ratio. The software removes pixel outliers, does statistics on the non outlier pixels, subtracts background from features and flags any outlier features. The software was then used to perform a LOWESS (locally weighted linear regression analysis) dye normalisation and to calculate a p-value for each feature.   Data analysis was performed with Genespring GX 7.3.1. (Agilent, Palo Alto, CA, USA). Microarray data were imported into Genespring using Agilent’s two-colour ‘Enhanced FE’ import scenario which included ‘Per Spot: Divide by control channel’ and ‘Per Chip: Normalize to 50th percentile’ normalisation steps. Filters applied to the data to improve the quality of the normalised dataset include; Firstly, filtering ‘on flags’ such that any probes that were not deemed ‘present or marginal’ (according to feature extraction spot quality guidelines) in at least 22 of the 44 arrays were omitted from analysis. Second, probes that did not have a minimum threshold of 300 raw intensity units in at least 22 of 44 arrays were also omitted from analysis. The raw intensity cut off value of 300 was determined based on the calculation of base over proportional (C=a/b) calculation, which is calculated by plotting the standard deviation of normalised values against the control values. The point at which the curve flattens out is where the data measurement becomes reliable or where C (control strength) = a/b (where a = base and b = the proportional coefficient).

organism: Bos taurus

label_protocol: One ug of RNA was amplified using the amino Allyl MessageAmp ™ aRNA Kit (Ambion, 2130 Woodward St, Austin TX, 78744) to generate amino allyl modified aRNA for use in microarray hybridisation.  aRNA quantity was measured by spectrophotometry using a ND-1000 (Nanodrop Technologies, Wilmington, DE).  Five ug of aRNA was then vacuum dried and labelled with Cy3 and Cy5 NHS ester dyes (Amersham Cy3 and Cy5 Mono-Reactive Dye Packs, GE Healthcare UK Ltd., Little Chalfont, Buckinghamshire). Labelled aRNA was then purified on column, quantified and dye coupling efficiency measured using the Nanodrop (Nanodrop Technologies, Wilmington, DE) instrument.

extract_protocol: Endometrial tissue was homogenised in Qiagen buffer RLT (QIAGEN GmbH, QIAGEN, Hilden, Germany) using FastPrep Lysing Matrix D tubes in a FastPrep instrument (MP Biomedicals, Solon, OH).   Total RNA was extracted using a Qiagen RNeasy kit (QIAGEN). All samples were DNase treated using the Ambion DNA-free kit (Ambion, Austin, TX) according to the manufacturer’s instructions. RNA quantity was determined by spectrophotometry in a Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE). RNA integrity was checked using the Agilent 2100 Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA).

treatment_protocol: All Animals had estrous cycles syncronised with 12 animals receiving grade 1 embryo transfers at day 7 of the reproductive cycle, animals were then slaughtered at day 17 of the reproductive cycle and endometrial tissue samples obtained.

tag: tissue type

value: caruncular endometrium

tag: reproductive state

value: pregnant

tag: embryo size

value: Large (>20cm and >75mg)

source_name: Pooled endometrial tissue

value: intercaruncular and caruncular endometrium

value: pregnant and non-pregnant (cycling)


title: Adult worms treated Tris 10nM pH 8,8 (vehicle) during 24hs rep 1 (Control sample 1) cy5

description: No additional information


title: Intercaruncular_Pregnant_9790_Sub-fertile

value: intercaruncular endometrium


title: Caruncular_Pregnant_926_Fertile (repeat)


title: Caruncular_Pregnant_3807_Sub-fertile

value: Small (<20cm and <40mg)


title: Caruncular_Pregnant_9921_Sub-fertile


title: Caruncular_Pregnant_932_Fertile


title: Caruncular_Pregnant_3805_Sub-fertile


title: Caruncular_Pregnant_977_Sub-fertile


title: Caruncular_Pregnant_9246_Fertile


title: Adult worms treated with human TNF-alpha during 24hs rep 2 cy5

description: No additional information


title: Caruncular_Pregnant_3803_Sub-fertile


title: Caruncular_Pregnant_3957_Fertile


title: Caruncular_Pregnant_926_Fertile


title: Caruncular_Pregnant_3956_Fertile


title: Intercaruncular_Pregnant_1943_Fertile


title: Intercaruncular_Pregnant_3957_Fertile


title: Caruncular_Pregnant_1943_Fertile


title: Heart_RightVentricle_rep2

city: Montpellier

first: Laurent

last: Journot

address: 141 rue de la Cardonille

country: France

institute: MGX - Montpellier GenomiX

description:
Real-time RT-PCR
The expression levels of genes were determined by quantitative PCR using SYBR Green and an ABI Prism 7500 machine. Primer pairs did not span introns and were validated using mouse genomic DNA as a template. Primers giving at least 90% efficacy, as well as single amplicons with an appropriate melting temperature and size, were selected and further validated on a pool of cDNAs from different mouse tissues. No amplicons were generated from RT-minus samples. Experiments were performed on 1/700th of the cDNA product using 1X SYBR Green PCR Master Mix TaqMan PCR buffer from Applied Biosystems and 300nM of each primer pair. The cycling conditions included a hot start for 10 min at 95°C, followed by 40 cycles at 95°C for 15 s, and 60°C for 1 min and a final cycle of 95°C for 15s, 60°C for 1 min and 95°C for 15s.

data_processing: Data were analyzed using the threshold cycle (Ct) relative quantification method. Three HKGs among the eight tested, Hypoxanthine guanine phosphoribosyl transferase (HPRT), 2 microglobuline (µ2M) and Beta-Glucuronidase (GUS), were chosen to normalize the results, using the geNorm method (Vandesompele et al, 2002). The expression level of each gene was normalized according to the formula: 2-(Ct (gene)-arithmetic mean (Ct(HPRT),Ct(µ2M),Ct(GUS)) X100. Results are expressed as the percentage relative to the geometric average of the expression levels of the three selected House Keeping Genes (HKGs).

organism: Mus musculus

source_name: Heart, Right ventricule

extract_protocol:
RNA extraction and reverse transcription
Twenty hearts were dissected from 8-week-old C57BL/6 male mice. Total RNAs were prepared from pooled cardiac chambers: right atria (RA) including the SAN, left atria (LA), right (RV) and left ventricles (LV), using the Trizol method. RNAs were treated with DNase I RNase-Free and purified by LiCl precipitation. Three independent reverse transcriptions (RT) were performed using 3.5 µg of total RNA with random primers and the Mo-MuLV reverse transcriptase.

tag: Strain

tag: Gender

value: male

tag: Age

value: 8 weeks

tag: Tissue

value: heart


title: Adult worms treated Tris 10nM pH 8,8 (vehicle) during 1h rep 2 (Control sample 2) cy5

description: No additional information


title: Intercaruncular_Pregnant_3803_Sub-fertile


title: Heart_RightVentricle_rep3


title: Heart_LeftVentricle_rep3

source_name: Heart, Left ventricule


title: Heart_RightVentricle_rep1


title: Intercaruncular_Pregnant_3805_Sub-fertile


title: Heart_RightAtrium_rep3

source_name: Heart, Right atrium


title: Intercaruncular_Pregnant_9921_Sub-fertile


title: Intercaruncular_Pregnant_977_Sub-fertile


title: Heart_RightAtrium_rep2


title: Intercaruncular_Pregnant_926_Fertile


title: Heart_RightAtrium_rep1


title: Intercaruncular_Pregnant_3956_Fertile


title: Heart_LeftVentricle_rep1


title: Heart_LeftAtrium_rep1

source_name: Heart, Left atrium


title: Intercaruncular_Pregnant_9246_Fertile


title: PMBC_Control_rep4

status: Public on Sep 30 2009

city: Tainan

first: Chang-yi

last: Lin

address: No.1, University Road

department: institute of basic medical science

country: Taiwan

institute: National Cheng Kung University

description: PCR Arrays are the most reliable tools for analyzing the expression of a focused panel of genes. Each 96-well or 384-well plate includes SYBR Green-optimized primer assays for a thoroughly researched panel of relevant, pathway- or disease-focused genes. PCR Arrays can also be customized to contain a panel of genes tailored to your specific research interests. Our high-quality primer design and master mix formulation enable the PCR Array to amplify 96 or 384 different gene-specific products simultaneously under uniform cycling conditions. This combination provides the PCR Array with the specificity and the high amplification efficiencies required for accurate real-time SYBR Green results. The simplicity of the PCR Arrays makes them accessible for routine use in every research laboratory.

scan_protocol: ABI 7900 hardware http://www.sabiosciences.com/support_manual.php

data_processing: Ct value was analysis by SDS 2.2 software directly. ΔCt=Ct(target gene)-Ave Ct(H1~H5). H1~H5 were house keeping genes. Normalized value=2^-ΔCt

molecule: polyA RNA

organism: Homo sapiens

source_name: peripheral mononuclear blood cells from Control

treatment_protocol: without any stimulation

tag: gender

value: female

tag: age

tag: tissue

value: peripheral mononuclear blood cells


title: Intercaruncular_Pregnant_3807_Sub-fertile


title: PMBC_Control_rep5


title: Intercaruncular_Pregnant_932_Fertile


title: PMBC_Case_rep2

source_name: peripheral mononuclear blood cells from PVL case


title: PMBC_Case_rep4


title: Heart_LeftVentricle_rep2

tag: Description :


title: PMBC_Case_rep3


title: PMBC_Control_rep2


title: PMBC_Control_rep3


title: PMBC_Control_rep1


title: PMBC_Case_rep1


title: PMBC_Case_rep5


title: Heart_LeftAtrium_rep2


title: Heart_LeftAtrium_rep3


title: ERaKO whole embryo 2

status: Public on Jul 22 2009

city: bukyo-ku

first: kaoru

last: yamagata

state: Tokyo

address: yayoi 1-1-1

country: Japan

institute: university of tokyo

description: Standard Taqman Assay: Quantitative real-time PCR was performed using Applied Biosystems 7900HT system and universal cycling conditions (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles).

data_processing: Data was processed using SDS 2.3 software (Applied Biosystems, Foster City, CA). Normalized by subtracting mammu6 to get Delta CT

label: FAM

source_name: ERalpha KO mice whole embryo

label_protocol: Standard TaqMan protocol

extract_protocol: Total RNA was isolated from embryo using TRIzol (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions.

tag: strain

value: whole embryo

tag: genotype

value: ER-alpha KO


title: ERaKO whole embryo 1


title: WT whole embryo 1

source_name: WT whole embryo

value: wild-type


title: WT whole embryo 2


title: MF3-9_lymphoma_Rep2

status: Public on Jul 01 2009

city: Albuquerque

first: Matthew

middle: Luke

last: Fero

state: NM

address: 1201 Camino de Salud

department: Internal Medicine

country: USA

institute: University of New Mexico

description: MuMLV induced T-cell lymphoma or normal mouse thymus are compared to a pooled RNA reference.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing:
# To download GEO data;
array.getGEO(GSE = "GSE16005") ;
# Load raw data into R;
data.raw <- array.readGEO(type = "raw");
# Load normalized data into R;
data.norm <- array.readGEO(type = "norm");
# Recapitulate normalization routine (optional);
data.normL <- array.norm(data.raw2, norm1 = "l", MADscale = FALSE, Filter = TRUE, span1 = 0.4) ;
data.normLT <- array.norm(data.normL, norm1 = "t", span1 = 0.25, MADscale = FALSE, Filter = TRUE) ;
data.normLTS <- array.swap(data.normLT, NoS = !data.norm@maTargets@maInfo$Swap, Sw = data.norm2@maTargets@maInfo$Swap);
#;
######## BEGIN Comments ####### ;
# The preceding is an R script to download raw GSM data and to generate normalized log ratios ;
# In summary the script:
#   1) Downloads the data to a series of temporary objects (GSE.parsed, GSE.headers, GSE.call)
#   2) Generates a marrayRaw object called, 'data.raw'.
#   3) Performs sequential normalization step:
#      a) Intensity dependent loess,
#      b) 2D-location dependent loess,
#      c) Inversion of channels with dye-reversal. ;
# The script requires a custom R package 'ArrayFun'. ;
# URL: http://labs.fhcrc.org/fero/R/ArrayFun.html ;
# Also requires 'marray' package (http://www.bioconductor.org). ;
# Source the script, above, to normalize the data. ;
# Returns two R objects: data.raw and data.norm. ;
# data.norm@maM contains the log(2) normalized values. ;
# See ?ArrayFun for details. ;
######### END Comments ######## ;

label_protocol: Custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: TRIzol extraction with 75% isopropanol precipitation of RNA. DNAseI digestion followed by Qiagen RNeasy mini column purification.

tag: disease state

value: lymphoma

value: tumor

tag: specimen

value: FALSE

tag: sex

value: Female

value: 22.1 weeks

source_name: control pool

tag: reference

value: equal amounts of RNA from of all samples were pooled as a common reference


title: MF3-4_lymphoma_Rep2

value: TRUE

value: 17.4 weeks


title: MF3-2_lymphoma_Rep2

value: 19.3 weeks


title: MF3-31_lymphoma_Rep1

value: Male

value: 50.9 weeks


title: MF3-1_lymphoma_Rep1

value: 19.7 weeks


title: MF3-33_lymphoma_Rep2

value: 18.6 weeks


title: MF3-6_lymphoma_Rep1

value: 21.7 weeks


title: MF3-31_lymphoma_Rep2


title: MF3-4_lymphoma_Rep1


title: MF3-33_lymphoma_Rep1


title: MF3-12_lymphoma_Rep2

value: 17 weeks


title: MF3-2_lymphoma_Rep1


title: MF3-39_normal_Rep2

value: normal

value: thymus

value: 44.6 weeks


title: MF3-9_lymphoma_Rep1

value: lymphoma

value: tumor


title: MF3-1_lymphoma_Rep2

value: FALSE

value: Female


title: MF3-13_lymphoma_Rep2

value: 17.9 weeks

value: equal amounts of RNA from of all samples were pooled as a common reference


title: MF3-13_lymphoma_Rep1

value: TRUE


title: MF3-6_lymphoma_Rep2


title: MF4-14_lymphoma_Rep2

value: 20 weeks


title: MF3-39_normal_Rep1

value: Male


title: MF3-12_lymphoma_Rep1


title: MF3-18_lymphoma_Rep2

value: 31 weeks


title: MF4-14_lymphoma_Rep1


title: MF3-16_lymphoma_Rep1

value: 33.9 weeks


title: MF3-17_lymphoma_Rep1

value: 35.9 weeks


title: MF3-17_lymphoma_Rep2


title: MF3-16_lymphoma_Rep2


title: MF3-18_lymphoma_Rep1


title: MF3-19_normal_Rep2

value: 6 weeks


title: Relative miRNA expression_Differentiation day5 vesus day1

status: Public on Jun 13 2009

city: San Antonio

first: Yongxin

last: Chen

state: TX

address: 7703 Floyd Curl Drive

department: Surgery

institute: University of Texas Health Science Center at San Antonio

data_processing: Cycle threshold (Ct) values were calculated with SDS software v.2.3 using automatic baseline settings and a threshold of 0.2. The comparative Ct method was used to calculate the relative miRNA expression. The Ct value of an endogenous control gene (MammU6, snRNA) was subtracted from the corresponding Ct value for the target gene resulting in the ΔCt value. Relative miRNA expression was determined by 2^-ΔΔCt.

source_name: myogenic progenitor cells (MPC)

growth_protocol: Cells were cultured in primary GM containing Ham's F-10 (Invitrogen, Carlsbad, CA), 20% FBS (VWR, West Chester, PA), 10 ng/ml FGF-2 (Promega, Madison WI), 100 U/ml penicillin G, and 100 µg/ml streptomycin (Invitrogen, Carlsbad, CA) and grown on type I collagen (0.1 mg/ml, Sigma Aldrich, St. Louis, MO)-coated tissue culture plates. All analyses were performed with primary MPC cultures at passage 3.

extract_protocol: Total RNA was isolated from MPC cells using TRIzol (Invitrogen) according to manufacturer’s instructions. RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies) and RNA samples with RNA integrity number (RIN) > 9 were used in the array studies.

treatment_protocol:
For MPC proliferation, cells were cultured in growth medium (GM) and plated on type I collagen-coated flasks at a density of 5 x 10^5 cells/T25 flask (Sigma, St Louis, MO).
For MPC differentiation, cells were seeded on entactin-collagen IV-laminin (ECL, 5 µg/cm2, Millipore)-coated plates at a density of 4 x 10^5 cells/60 mm dish, allowed to adhere for 24 hrs in GM (day 0), and switched to differentiation medium (DM) composed of 2% horse serum (Invitrogen), 100 U/ml penicillin and 100 µg/ml streptomycin in DMEM.

value: hind limb muscle

tag: cell type

value: myogenic progenitor cells (MPC)

tag: protocol

value: differentiation assay


title: Relative miRNA expression_Proliferation day2 vesus day5

value: proliferation assay


title: Amp2_ArrayB

status: Public on May 13 2009

first: Jonathan

middle: Adam

last: Gelfond

address: Mail Code 7933, 7703 Floyd Curl

department: Epidemiology & Biostatistics

institute: UT Health Science Ctr San Antonio

source_name: Proliferating C2C12 cells

growth_protocol: Mouse C2C12 myoblasts were cultured in growth media containing Dulbecco's Modified Eagle Medium (DMEM) (ATCC), supplemented with 10% fetal bovine serum (FBS) (Hyclone, Logan, UT) and 1% penicillin-streptomycin (Mediatech, Inc., Herndon, VA) at 37°C in a humidified atmosphere of 5% CO2 in air.

extract_protocol: Total RNA was isolated from proliferating C2C12 cells using TRIzol (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions. Total RNA concentration was quantified by an absorbance at 260 nm using a SmartSpec 3000 spectrophotometer (Bio-Rad, Hercules, CA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and samples with RNA integrity number (RIN) >9 were used in the array studies. Aliquots of the same RNA sample were used for all the experiments in both the microarray and qPCR-array measurements.

value: muscle

value: myoblast

value: amplification


title: NonAmp2_ArrayB

value: no amplification


title: Relative miRNA expression_Differentiation day2 vesus day1


title: Relative miRNA expression_Differentiation day1 vesus day0

source_name: Primary myogenic progenitor cells (MPC)

value: myogenic progenitor cell (MPC)


title: Relative miRNA expression_Differentiation day5 vesus day2


title: Relative miRNA expression_Differentiation day5 vesus day0


title: Relative miRNA expression_Differentiation day2 vesus day0


title: MF3-25_lymphoma_Rep1

value: equal amounts of RNA from of all samples were pooled as a common reference

value: lymphoma

value: tumor

value: FALSE

value: 25.6 weeks


title: Amp1_ArrayB


title: MF3-27_lymphoma_Rep2

value: TRUE

value: Female

value: 26.1 weeks


title: MF3-24_lymphoma_Rep1

value: 21.9 weeks


title: MF3-25_lymphoma_Rep2

value: Male


title: MF3-28_lymphoma_Rep2

value: 20.3 weeks


title: Day2-RT2-ArrayA

tag: time

value: day 2

value: aliquot 2


title: Day2-RT1-ArrayA

value: muscle

value: myoblast

value: aliquot 1


title: MF3-22_normal_Rep1

value: normal

value: thymus

value: 6 weeks


title: MF3-22_normal_Rep2

value: equal amounts of RNA from of all samples were pooled as a common reference


title: MF3-24_lymphoma_Rep2

value: lymphoma

value: tumor

value: FALSE


title: MF3-19_normal_Rep1

value: Female


title: MF3-27_lymphoma_Rep1

value: TRUE

value: 26.1 weeks


title: wt_d26_rep1

status: Public on May 15 2009

city: Houston

first: JoAnne

last: Richards

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
Gene expression data.
Replicate 1 of 2.

hyb_protocol: cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station 450 automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner 3000 and quantified with Affymetrix GCOS 1.4.

data_processing: The data were analyzed using affy package from Bioconductor with RMA method.

label: biotin

source_name: ovary from 26-day-old wild type mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Animals were housed under a 16-h light/8-h dark schedule in the Center for Comparative Medicine at Baylor College of Medicine and provided food and water ad libitum.

extract_protocol: Total RNA extraction by RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Animals were treated in accordance with the NIH Guide for the Care and Use of Laboratory Animals, as approved by the Animal Care and Use Committee at Baylor College of Medicine.

value: ovary

value: wild type

value: 26 days


title: wt_d26_rep2

description:
Gene expression data.
Replicate 2 of 2.


title: MF3-28_lymphoma_Rep1

value: 20.3 weeks


title: Sample_12_4_hours_BAA_dna damage

status: Public on Apr 08 2009

city: Urbana

first: Michael

middle: J

last: Plewa

state: IL

address: 1101 W Peabody Dr

department: Crop Sciences

institute: University of Illinois at Urbana-Champaign

description: This is a 4 hours 60 µM Bromoacetic acid treated sample. FHs 74 small intestinal cells (female 3 to 4 months gestation normal small intestine cells).

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: The value colum is the diference between the Raw value and the averga of the Housekeeping genes for that sample (ID HO1 to HO5)

source_name: FHs 74 int cells RNA after 4 hours treatment (BAA)

label_protocol: not applicable

growth_protocol: Non-transformed human small intestine epithelial cells, line FHs 74 Int, were purchased from American Type Culture Collection (ATCC) (Manassas, Va). The FHs cells were maintained in Hybri-Care medium ATCC 46-X containing 10% fetal bovine serum (FBS), 1% antibiotic (10 units/mL penicillin G sodium, 10 μg/mL streptomycin sulfate, 25 µg/mL amphotericin B, 0.85% saline), and 30 ng/mL human epidermal growth factor (EGF) at 37°C in a humidified atmosphere of 5% CO2. Medium was changed every 2-3 days to supply ample EGF for continued growth.

extract_protocol: After the 30 min and 4 h exposures to bromoacetic acid cell suspensions were harvested and trans-ferred to RNase-free microfuge tubes and centrifuged at 300×g for 5 min. An aliquot of each cell suspension was reserved, prior to centrifugation, for acute cytotoxicity and SCGE analysis. The supernatant was removed and RNA isolation was conducted using a Qiagen RNeasy Mini Kit (Valencia, CA) following the recommended protocol for animal cell isolation

treatment_protocol: 4 Hours 60 µM Bromoacetic acid treated (46-X medium)

tag: cell line

value: FHs 74


title: Day1-RT2-ArrayA

value: muscle

value: myoblast

value: day 1

value: aliquot 2


title: Sample_12_4_hours_BAA_toxic_response

treatment_protocol: 4 hours 60 µM Bromoacetic acid treated (46-X medium)


title: Sample_10_4_hours_BAA_toxic_response


title: Sample_9_4_hours_control_dna damage

description: This is a 4 hours control sample. FHs 74 small intestinal cells (female 3 to 4 months gestation normal small intestine cells).

source_name: FHs 74 int cells RNA after 4 hours treatment (control)

treatment_protocol: 4 Hours control (46-X medium no Bromoacetic acid)


title: Sample_11_4_hours_BAA_dna damage


title: Sample_7_4_hours_control_toxic_response


title: Sample_11_4_hours_BAA_toxic_response


title: Sample_8_4_hours_control_toxic_response


title: Sample_7_4_hours_control_dna damage

treatment_protocol: 4 hours control (in 46-X medium)


title: Sample_10_4_hours_BAA_dna damage


title: Sample_9_4_hours_control_toxic_response


title: Sample_4_30_minutes_BAA_toxic_response

description: This is a 30 minutes BAA 60 µM treated sample. FHs 74 small intestinal cells (female 3 to 4 months gestation normal small intestine cells).

source_name: FHs 74 int cells RNA after 30 minutes treatment (BAA)

treatment_protocol: 30 minutes 60 µM Bromoacetic acid  treated (in 46-X medium Bromoacetic acid)


title: Sample_3_30_minutes_control_dna damage

description: This is a 30 minutes control sample. FHs 74 small intestinal cells (female 3 to 4 months gestation normal small intestine cells).

source_name: FHs 74 int cells RNA after 30 minutes treatment (control)

treatment_protocol: 30 minutes control (46-X medium no Bromoacetic acid)


title: Sample_4_30_minutes_BAA_dna damage

description: This is a 30 minutes 60 µM Bromoacetic acid treated sample. FHs 74 small intestinal cells (female 3 to 4 months gestation normal small intestine cells).

treatment_protocol: 30 minutes 60 µM Bromoacetic acid treated (46-X medium)


title: Sample_5_30_minutes_BAA_dna damage


title: Sample_1_30_minutes_control_dna damage


title: Sample_5_30_minutes_BAA_toxic_response


title: Sample_3_30_minutes_control_toxic_response

treatment_protocol: 30 minutes control (46-X medium without Bromoacetic acid)


title: Sample_6_30_minutes_BAA_toxic_response


title: Sample_2_30_minutes_control_dna damage


title: Sample_8_4_hours_control_dna damage


title: Sample_2_30_minutes_control_toxic_response


title: Sample_1_30_minutes_control_toxic_response


title: Sample_6_30_minutes_BAA_dna damage


title: CB15N in M2I vs. CB15N in M2G

status: Public on Dec 20 2008

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

description: Sample compares mRNA expression in Caulobacter strain CB15N grown in M2-Glucose versus M2-Inositol.

data_processing: The mean background was subtracted from the mean signal for each channel. The background-subtracted Cy5 signal was divided by the background-subtracted Cy3 signal, and the log base 2 of this ratio was used as the value in the tables.

organism: Caulobacter vibrioides

source_name: CB15N grown in M2-Inositol

extract_protocol: Cultures were spun down at 10,000 x g for 30 seconds, the supernatant was removed, and the cell pellets were flash frozen in liquid nitrogen.  RNA was isolated from these cells by incubating in 1 ml of Trizol (Invitrogen, Carlsbad, CA) at 65°C for 10 minutes, adding chloroform, vortexing, spinning, and extracting the aqueous layer.  Nucleic acid in the aqueous layer was isopropanol precipitated overnight at -80°C followed by a 30 minute centrifugation at 16,000 x g.  The ethanol-washed and air-dried nucleic acid pellet was resuspended in 50 μl of nuclease-free water (IDT, Coralville, IA).  1 μl of RNase-free DNase I (Ambion, Austin, TX) was added to the sample and incubated at room temperature for two hours to remove any residual DNA.  The nucleic acid in this digested sample was then acid phenol-chloroform (Ambion, Austin, TX) extracted, ethanol precipitated at -80°C overnight, and centrifuged at 16,000 x g to produce a DNA-free RNA pellet.  RNA quality was assessed via agarose gel electrophoresis and RNA concentration determined by UV spectrophotometry using a Shimadzu UV-1650 (Kyoto, Japan).

tag: Exponential phase culture of Caulobacter strain CB15N grown in M2-Inositol media.

source_name: CB15N grown in M2-Glucose

tag: Exponential phase culture of Caulobacter strain CB15N grown in M2-Glucose media.


title: Sample_9_control_3_4_hours_H2S_DNA_Signaling

status: Public on Oct 10 2008

first: H

middle: Rex

last: Gaskins

address: 1207 W Gregory dr

department: Institute for Genomic Biology

institute: University of Illinois

description: This is a 4 hour control sample.

source_name: human intestinal epithelial FHs 74 Int cells (ATCC CCL-241)

growth_protocol: FHs cells were maintained in Hybri-Care medium ATCC 46-X containing 10% FBS, 1% antibiotic (10 units/mL penicillin G sodium, 10 μg/mL streptomycin sulfate, 25 μg/mL amphotericin B, 0.85% saline), and 30 ng/mL human EGF at 37°C in a humidified atmosphere of 5% CO2. Medium was changed every 2-3 days to supply ample EGF for continued growth.

extract_protocol: RNA was isolated using a Qiagen RNeasy Mini Kit (Valencia, CA) following the recommended protocol for animal cell isolation. To generate a high RNA yield, cell suspensions were pooled from 2 wells. DNase treatment of the RNA samples was conducted using Ambion DNA-free DNase (Austin, TX) according to manufacturer specifications. RNA concentrations were determined using the NanoDrop 1000 from Thermo Fisher Scientific (Wilmington, DE). The resulting genomic DNA-free RNA was concentrated by vacuum centrifugation for 15 minutes using the Speedvac system AE52010 from Savant (Halbrook, NY). RNA quantity was determined using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). RNA Integrity Numbers (RIN) were in the range from 8.6 to 9.9 (RNA quality for microarray analysis must have RIN values greater than 7)

treatment_protocol: control cells (untreated). Four days previous to the experiment, 4 x 10^5 FHs 74 Int cells were seeded in each well in six well plates. After a 4 hours, cells were washed twice with HBSS, harvested with trypsin, transferred to RNase-free 1.5 mL centrifuge tubes and centrifuged at 300× g for 5 minutes. An aliquot of each cell suspension was retained, prior to centrifugation, for acute cytotoxicity and SCGE analyses.

tag: The FHs 74 Int cells (ATCC CCL-241) are small intestine normal epithelial cells.


title: Sample_10_500uM_H2S_1_4_hourss_H2S_DNA_Signaling

description: This is a 4 hour 500 uM H2S treated sample.

treatment_protocol: Four days previous to the experiment, 4 x 10^5 FHs 74 Int cells were seeded in each well in six well plates. After a 4 hours of treatment with 500 uM H2S, cells were washed twice with HBSS, harvested with trypsin, transferred to RNase-free 1.5 mL centrifuge tubes and centrifuged at 300× g for 5 minutes. An aliquot of each cell suspension was retained, prior to centrifugation, for acute cytotoxicity and SCGE analyses.


title: Sample_11_500uM_H2S_2_4_hours_H2S_DNA_Signaling


title: Sample_7_control_1_4_hours_H2S_DNA_Signaling

description: This is a 4 hour control sample.


title: Sample_8_control_2_4_hours_H2S_DNA_Signaling

description: This is a 4 hour control sample.


title: CB15N in M2G vs. CB15N in M2I


title: S mansoni adult worms mice immunized with Sm29 antigen right replicate1

status: Public on Dec 18 2008

city: Campos dos Goytacazes

first: Thiago

middle: Motta

last: Venancio

state: RJ

address: Av Alberto Lamego 2000

institute: UENF

description: no additional information

scan_protocol: Slides were air dried and scanned using a microarray dual channel laser scanner (GenePix 4000B, Molecular Devices, USA) at 5 Ìm resolution, 100 % laser power and PMT levels were adjusted in order to obtain similar average intensities of red and green signal.

data_processing: Data was extracted from images using the Array Vision 8.0 program. Unreliable spots, having intensities too similar to local background (ie, low intensity) or saturated, were filtered out. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus A plot

source_name: S. mansoni adult worms recovered from mice vaccinated with Sm29 antigen

label_protocol: One microgram of total RNA from each sample was amplified using the T7-RNA polymerase-based linear amplification protocol. Three micrograms of aminoallyl-modified amplified RNA was labeled with Cy3 or Cy5 by indirect labeling (GE Healthcare). The Cy3- and Cy5-labeled samples were then combined, dried and re-suspended in hybridization buffer (50 % formamide, 25 % RNase free water and 25 % Microarray Hybridization buffer 4x from GE Healthcare).

extract_protocol: Total RNA was obtained using Trizol reagent (Invitrogen) according to the manufacturer's instructions. The RNA was quantified using the Nanodrop ND-1000 UV/Vis spectrophotometer and RNA integrity was checked by electrophoresis with an Agilent 2100 Bioanalyzer.

tag: The Schistosoma mansoni adult worms were recovered forty five days after infection of female C57BL/6 mice vaccinated three times with 25 µg of rSm29 plus adjuvant (using intervals of fifteen days between the vaccinations).

source_name: S. mansoni adult worms vaccinated with PBS plus adjuvant.

tag: The Schistosoma mansoni adult worms were recovered forty five days after infection of female C57BL/6 mice vaccinated three times with PBS plus adjuvant.


title: Sample_5_500uM_H2S_2_30_Minutes_H2S_DNA_Signaling

description: This is a treated sample sample.

treatment_protocol: Four days previous to the experiment, 4 x 10^5 FHs 74 Int cells were seeded in each well in six well plates. After a 30 minutes of treatment with 500 uM H2S, cells were washed twice with HBSS, harvested with trypsin, transferred to RNase-free 1.5 mL centrifuge tubes and centrifuged at 300× g for 5 minutes. An aliquot of each cell suspension was retained, prior to centrifugation, for acute cytotoxicity and SCGE analyses.


title: Sample_6_500uM_H2S_3_30_Minutes_H2S_DNA_Signaling

description: This is a treated sample sample.


title: SAGE White Blood Cells monocyte depleted mononuclear cells normal AP A1

status: Public on Mar 20 2009

type: SAGE

anchor: NlaIII

city: Bethesda

first: Cancer Genome Anatomy Project

last: CGAP

state: MD

department: Cancer Genome Anatomy Project

institute: National Cancer Institute

description:
CGAP_Numeric_library_ID: 1576
Tagging_enzyme: Mme I
Library_producer: Willmar D. Patino, Cardiovascular Branch-NHLBI
Laboratory: Paul M. Hwang, Cardiovascular Branch-NHLBI

source_name: white blood cell, monocyte-depleted mononuclear cells, normal, antibody purified, male, adult, extracted short sage

tag: organ/tissue

value: white blood cells

tag: tissue preparation

value: antibody purified

tag: age

value: male

value: monocyte-depleted mononuclear cells

tag: mutations


title: Sample_12_500uM_H2S_3_4_hours_H2S_DNA_Signaling


title: Sample_4_500uM_H2S_1_30_Minutes_H2S_DNA_Signaling

description: This is a treated sample sample.

treatment_protocol: Four days previous to the experiment, 4 x 10^5 FHs 74 Int cells were seeded in each well in six well plates. After a 30 minutes of treatment with 500 uM H2S cells were washed twice with HBSS, harvested with trypsin, transferred to RNase-free 1.5 mL centrifuge tubes and centrifuged at 300× g for 5 minutes. An aliquot of each cell suspension was retained, prior to centrifugation, for acute cytotoxicity and SCGE analyses.


title: SAGE White Blood Cells monocyte depleted mononuclear cells normal AP P1

description:
CGAP_Numeric_library_ID: 1575
Tagging_enzyme: Mme I
Library_producer: Willmar D. Patino, Cardiovascular Branch-NHLBI
Laboratory: Paul M. Hwang, Cardiovascular Branch-NHLBI


title: Sample_3_control_3_30_Minutes_H2S_DNA_Signaling

description: This is a control sample.

treatment_protocol: control cells (untreated). Four days previous to the experiment, 4 x 10^5 FHs 74 Int cells were seeded in each well in six well plates. After a 30 minutes in medium without FBS cells were washed twice with HBSS, harvested with trypsin, transferred to RNase-free 1.5 mL centrifuge tubes and centrifuged at 300× g for 5 minutes. An aliquot of each cell suspension was retained, prior to centrifugation, for acute cytotoxicity and SCGE analyses.


title: LSAGE White Blood Cells monocyte depleted mononuclear cells normal AP P1

description:
CGAP_Numeric_library_ID: 1568
Tagging_enzyme: Mme I
Library_producer: Willmar D. Patino, Cardiovascular Branch-NHLBI
Laboratory: Paul M. Hwang, Cardiovascular Branch-NHLBI
References: W. D. Patino et al., Proc Natl Acad Sci U S A 102, 3423-3428 (2005) [PUBMED=15728378]

source_name: white blood cell, monocyte-depleted mononuclear cells, normal, antibody purified, male, adult, long sage


title: mSAGE Vascular endothelium 72hr regenerating liver associated AP 72hrRLiEC

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2202
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]

source_name: vascular, normal, endothelium, antibody purified, extracted short sage, adult

value: vascular

value: unknown


title: mSAGE Vascular endothelium 24hr regenerating liver associated AP 24hrRLiEC

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2199
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: mLSAGE Vascular endothelium 72hr regenerating liver associated AP 72hrRLiEC

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2203
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]

source_name: vascular, normal, endothelium, antibody purified, long sage, adult


title: S mansoni adult worms mice immunized with Sm29 antigen right replicate2

description: no additional information

hyb_protocol: The Cy3- and Cy5-labeled samples were then combined, dried and re-suspended in hybridization buffer (50 % formamide, 25 % RNase free water and 25 % Microarray Hybridization buffer 4x from GE Healthcare).


title: mLSAGE Vascular endothelium 24hr regenerating liver associated AP 24hrRLiEC

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2198
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: S mansoni adult worms mice immunized with Sm29 antigen right replicate4

description: no additional information


title: LSAGE White Blood Cells monocyte depleted mononuclear cells normal AP A1

description:
CGAP_Numeric_library_ID: 1569
Tagging_enzyme: Mme I
Library_producer: Willmar D. Patino, Cardiovascular Branch-NHLBI
Laboratory: Paul M. Hwang, Cardiovascular Branch-NHLBI
References: W. D. Patino et al., Proc Natl Acad Sci U S A 102, 3423-3428 (2005) [PUBMED=15728378]


title: mSAGE Vascular endothelium 48hr regenerating liver associated AP 48hrRLiEC

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2201
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: S mansoni adult worms mice immunized with Sm29 antigen right replicate3

description: no additional information


title: mLSAGE Vascular endothelium 48hr regenerating liver associated AP 48hrRLiEC

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2200
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: 13689488 - gollum_a vs WT_a

status: Public on Nov 01 2008

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

description: Elucidate the role of Gollum gene in the plant development by a RNAi approach

hyb_protocol: WT_a Cy5 / gollum_a Cy3 : 30pmol. 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,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,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: 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: leaf - media: soil hygrometry: 0.6 temperature: 22°C light: 16h/24h at 250µmol.m2.s-1

treatment_protocol: no treatment

tag: Arabidopsis thaliana (col-0)  - dev.stage (Boyes et al. Plant Cell 2001):6.00


title: 13689490 - gollum_b vs WT_b

hyb_protocol: WT_b Cy5 / gollum_b Cy3 : 30pmol. 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: 13689489 - WT_b vs gollum_b

hyb_protocol: gollum_b Cy5 / WT_b Cy3 : 30pmol. 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: 13689487 - WT_a vs gollum_a

hyb_protocol: gollum_a Cy5 / WT_a Cy3 : 30pmol. 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: Sample_1_control_1_30_Minutes_H2S_DNA_Signaling

description: This is a control sample.


title: Sample_11_500uM_H2S_2_4_hours_H2S_DNA_pathway_finder


title: Sample_12_500uM_H2S_3_4_hours_H2S_DNA_pathway_finder


title: Sample_10_500uM_H2S_1_4_hours_H2S_DNA_pathway_finder


title: Sample_2_control_2_30_Minutes_H2S_DNA_Signaling

description: This is a control sample.


title: Sample_9_control_3_4_hours_H2S_DNA_pathway_finder

description: This is a control sample.


title: Sample_8_control_2_4_hours_H2S_DNA_pathway_finder

description: This is a control sample.


title: Sample_3_control_3_30_Minutes_H2S_pathway_finder

description: This is a control sample.

growth_protocol: FHs cells were maintained in Hybri-Care medium ATCC 46-X containing 10% FBS, 1% antibiotic (10 units/mL penicillin G sodium, 10 μg/mL streptomycin sulfate, 25 μg/mL amphotericin B, 0.85% saline), and 30 ng/mL human EGF at 37°C in a humidified atmosphere of 5% CO2. Medium was changed every 2-3 days to supply ample EGF for continued growth


title: Sample_2_control_2_30_Minutes_H2S_pathway_finder

description: This is a control sample.


title: Sample_6_500uM_H2S_3_30_Minutes_H2S_DNA_pathway_finder

description: This is a treated sample.


title: Sample_4_500uM_H2S_1_30_Minutes_H2S_DNA_pathway_finder

description: This is a treated sample.


title: Sample_1_control_1_30_Minutes_H2S_pathway_finder

description: This is a control sample.


title: C57BL/6 wild-type mice; R848 treated Exp 1

status: Public on Sep 30 2008

city: Zuerich

first: Stefan

last: Baenziger

address: Raemisstrasse 100

department: Department of internal Medicine

country: Switzerland

institute: University Hospital Zurich

description:
Reverse transcription was performed with 5 Âµg  of total RNA in a total volume of 50 Âµl. RNA was incubated with 1250 ng of oligo(dT) primer (Life Technologies) and 500 ÂµM dNTPs (Roche) at 65Â°C for 5 min, followed by incubation on ice for 5 min. Samples were then incubated with 3 mM MgCl2 (Promega) and 60 U of RNase inhibitor (Roche) in 1x ImProm-II RT reaction buffer (Promega) at 42Â°C for 2 min. ImProm-II RT (500 U; Promega) was added, and reactions were performed at 42Â°C for 50 min, followed by inactivation at 65Â°C for 15 min. Residual RNA was digested with 1250 ng of RNase (Roche) at 37Â°C for 20 min.
	Gene expression was investigated by using mouse TLR pathway RTÂ² Profilerâ„¢ PCR Array and a Biorad iCycler according to the manufacturerâ€™s protocol. The plate includes positive, reverse transcription, and genomic DNA controls.
	In each reaction, 50 ng of total RNA was amplified in a final volume of 25 Âµl. Thermal cycling conditions were:  95Â°C for 10 min, followed by 40 cycles of 95Â°C for 15 s, and 60Â°C for 1 min.

data_processing:
Raw Data (i.e., Ct values) are shown.
Ct values >35 or blank was set to 35.

source_name: spleen

extract_protocol: splenic samples were immediately subjected to RNAlater (Qiagen) and stored at  20 Â°C until use. RNA was extracted from 20 mg of samples with the RNeasy mini-kit (Qiagen) according to the manufacturerâ€™s instructions. For tissue homogenates, blocks were disrupted with a mortar and pestle in lysis buffer containing 2-ME. After extraction, RNA was pooled from replicates (n = 3). To remove residual DNA, RNA preparations were treated with DNAfree (Ambion) according to the manufacturerâ€™s instructions. RNA quality, as judged by gel electrophoresis and spectrophotometry, was comparable in all samples.

treatment_protocol: Mice (n=3) were treated with 1mg/kg/d R848 or PBS (Mock) for 7 days.

tag: C57B/6 wild-type mice


title: Sample_5_500uM_H2S_2_30_Minutes_H2S_DNA_pathway_finder

description: This is a treated sample.


title: Sample_7_control_1_4_hours_H2S_DNA_pathway_finder

description: This is a control sample.


title: C57BL/6 wild-type mice; Mock treated Exp 2


title: TLR7-/- mice; R848 treated

data_processing:
Raw Data (i.e., Ct values) are shown.
Ct values >35 or blank was set to 35..

tag: Toll-like receptor (TLR) 7 k.o. mice


title: C57BL/6 wild-type mice; Mock treated Exp 1

description:
Reverse transcription was performed with 5 µg  of total RNA in a total volume of 50 µl. RNA was incubated with 1250 ng of oligo(dT) primer (Life Technologies) and 500 µM dNTPs (Roche) at 65°C for 5 min, followed by incubation on ice for 5 min. Samples were then incubated with 3 mM MgCl2 (Promega) and 60 U of RNase inhibitor (Roche) in 1x ImProm-II RT reaction buffer (Promega) at 42°C for 2 min. ImProm-II RT (500 U; Promega) was added, and reactions were performed at 42°C for 50 min, followed by inactivation at 65°C for 15 min. Residual RNA was digested with 1250 ng of RNase (Roche) at 37°C for 20 min.
Gene expression was investigated by using mouse TLR pathway RT² Profiler™ PCR Array and a Biorad iCycler according to the manufacturer’s protocol. The plate includes positive, reverse transcription, and genomic DNA controls.
In each reaction, 50 ng of total RNA was amplified in a final volume of 25 µl. Thermal cycling conditions were:  95°C for 10 min, followed by 40 cycles of 95°C for 15 s, and 60°C for 1 min.

extract_protocol: splenic samples were immediately subjected to RNAlater (Qiagen) and stored at  20 °C until use. RNA was extracted from 20 mg of samples with the RNeasy mini-kit (Qiagen) according to the manufacturer’s instructions. For tissue homogenates, blocks were disrupted with a mortar and pestle in lysis buffer containing 2-ME. After extraction, RNA was pooled from replicates (n = 3). To remove residual DNA, RNA preparations were treated with DNAfree (Ambion) according to the manufacturer’s instructions. RNA quality, as judged by gel electrophoresis and spectrophotometry, was comparable in all samples.


title: C57BL/6 wild-type mice; R848 treated Exp 2


title: IFNAR-/- mice; R848 treated

tag: Type I interferon receptor (IFNAR) k.o. mice


title: TLR7-/- mice; Mock treated

data_processing: Data generated by real-time quantitative PCR were normalized to Hypoxanthine guanine phosphoribosyl transferase 1, Heat shock protein 90kDa alpha, and Glyceraldehyde-3-phosphate dehydrogenase. Animals were tested once.


title: IFNAR-/- mice; Mock treated


title: RRE2 14028s(delpreAB)pBAD18 14028s(delpreAB)pBAD18preA LB10mMAra OD0.74 6D068_2

status: Public on Sep 23 2008

city: Irvine

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: biological replicate, Date_of_Scan = Fri Nov 04 09:03:24 2005

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv6_01_050607

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

label_protocol: incorporation of Cy3-dCTP with SuperscriptII and random hexamers

extract_protocol: Promega SV RNA isolation kit

tag: Salmonella enterica subsp. enterica serovar Typhimurium 14028s

tag: Salmonella typhimurium 14028s-preAB mutant complemented with pBAD18 (vector control) grown in LB+10mM Ara at OD0.74

label_protocol: incorporation of Cy5-dCTP with SuperscriptII and random hexamers

tag: Salmonella typhimurium 14028s-preAB mutant complemented with pBAD18+preA grown in LB+10mM Ara at OD0.74


title: RRE2 14028s(delpreAB)pBAD18 14028s(delpreAB)pBAD18preA LB10mMAra OD0.74 6D068_1

organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: RRE2 14028s(delpreAB)pBAD18 14028s(delpreAB)pBAD18preA LB10mMAra OD0.74 6D068_3


title: RRE2 14028s(wt)pBAD18preA 14028s(delpreA)pBAD18 LB10mMAra OD0.74_6D070_3

description: biological replicate, Date_of_Scan = Fri Nov 04 11:17:45 2005

tag: Salmonella typhimurium 14028s complemented with pBAD18+preA grown in LB+10mM Ara at OD0.74

tag: Salmonella typhimurium 14028s-preA mutant complemented with pBAD18 (vector control) grown in LB+10mM Ara at OD0.74


title: RRE2 14028s(delpreAB)pBAD18preA 14028s(delpreAB)pBAD18 LB10mMAra OD0.74 6D069_2

description: biological replicate, Date_of_Scan = Fri Nov 04 09:50:46 2005

label_protocol: incorporation of Cy3-dCTP with Reverse Transcriptase

label_protocol: incorporation of Cy5-dCTP with Reverse Transcriptase


title: RRE2 14028s(wt)pBAD18preA 14028s(delpreA)pBAD18 LB10mMAra OD0.74_6D070_1


title: RRE2 14028s(delpreA)pBAD18 14028s(wt)pBAD18preA LB10mMAra OD0.74_6D071_3

description: biological replicate, Date_of_Scan = Fri Nov 04 11:41:50 2005


title: Adult workers little bb Gp9 polygyne multiple colonies Georgia Louisiana 06

status: Public on Jun 06 2008

city: Lausanne

first: John

last: Wang

address: Batiment Biophore

department: Department of Ecology and Evolution

institute: University of Lausanne

description: Adult workers were randomly collected from the foraging area and frozen individually. RNA from 7-10 workers of the same genotype were pooled.

hyb_protocol: Hybridization buffer (3x SSC, 0.18% SDS, 200 ng/μl yeast tRNA, 200 ng/µl polyA DNA; final concentration) was added to samples; samples were denatured, applied to microarrays, and hybridized overnight at 64°C. After hybridization, slides were washed sequential.

scan_protocol: Scanner: Agilent Technologies microarray scanner. Image quantification GenePix 5.1

data_processing: printTipLoess normalization (marray, Bioconductor)

organism: Solenopsis invicta

source_name: Reference RNA batch 2006

label_protocol: Total RNA was amplified using the Ambion Message Amp II kit. Amplified RNA plus Alien spike control RNAs (Stratagene) were labeled using the indirect aa-dUTP labeling method. Reverse transcription primers: random 9mers.

extract_protocol: Total RNA extracted using Qiagen RNeasy Kit following manufacturer's instructions

tag: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)

source_name: Adult workers little bb Gp9 polygyne

tag: Genotype

value: little bb

tag: Colony form

value: polygyne

tag: Source population

value: Georgia and Louisiana


title: RRE2 14028s(wt)pBAD18preA 14028s(delpreA)pBAD18 LB10mMAra OD0.74_6D070_2


title: RRE2 14028s(delpreAB)pBAD18preA 14028s(delpreAB)pBAD18 LB10mMAra OD0.74 6D069_3


title: RRE2 14028s(delpreAB)pBAD18preA 14028s(delpreAB)pBAD18 LB10mMAra OD0.74 6D069_1


title: RRE2 14028s(delpreA)pBAD18 14028s(wt)pBAD18preA LB10mMAra OD0.74_6D071_2


title: RRE2 14028s(delpreA)pBAD18 14028s(wt)pBAD18preA LB10mMAra OD0.74_6D071_1


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 1days exp6547 rep3 87345

status: Public on Mar 28 2008

city: Mountain View

first: Jeremy

last: Gollub

address: 325 E. Middlefield Rd.

institute: Iconix Biosciences

description:
HybID: 87345
treated sample for experiment (RepID) 6547
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM222685: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_1days_exp6547_rep1_87343
Replicate experimental sample: GSM222686: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_1days_exp6547_rep2_87344
Matched control sample: GSM204657: LIVER_vehicle_NA_1days_control_NA_87149
Matched control sample: GSM204719: LIVER_vehicle_NA_1days_control_NA_87150
Matched control sample: GSM204697: LIVER_vehicle_NA_1days_control_NA_87151
Matched control sample: GSM204759: LIVER_vehicle_NA_3days_control_NA_87152
Matched control sample: GSM204796: LIVER_vehicle_NA_3days_control_NA_87153
Matched control sample: GSM204785: LIVER_vehicle_NA_3days_control_NA_87154
Matched control sample: GSM204871: LIVER_vehicle_NA_5days_control_NA_87155
Matched control sample: GSM204839: LIVER_vehicle_NA_5days_control_NA_87156
Matched control sample: GSM204861: LIVER_vehicle_NA_5days_control_NA_87215
Matched control sample: GSM204714: LIVER_vehicle_NA_1days_control_NA_87337
Matched control sample: GSM204637: LIVER_vehicle_NA_1days_control_NA_87338
Matched control sample: GSM204689: LIVER_vehicle_NA_1days_control_NA_87339
Matched control sample: GSM204793: LIVER_vehicle_NA_3days_control_NA_87340
Matched control sample: GSM204753: LIVER_vehicle_NA_3days_control_NA_87341
Matched control sample: GSM204778: LIVER_vehicle_NA_3days_control_NA_87342
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

hyb_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. 12.5 ug of cRNA sample was fragmented in 40 mM Tris-acetate (TrisOAc) pH7.9, 100 mM KOAc and 31.5 mM MgOAc at 94oC for 20 min. This typically resulted in a fragmented cRNA with a size range between 100 to 200 bases. 10 ug of the fragmented cRNA was used for hybridization of each Rat-Uniset I (RU1) Expression BioArray (Amersham Biosciences, Piscataway, NJ) in a volume of 260 ul, containing 78 ul of CodeLink Hyb buffer component A and 130 ul of CodeLink Hyb buffer component B (Amersham Biosciences, Piscataway, NJ). The hybridization solution was denatured at 90oC for 5 min then chilled on ice. The sample was vortexed at maximum speed for 5 sec and centrifuged at maximum speed for 5 min before 250 ul of the solution was injected into the inlet port of the flex-hybridization chamber, and placed in a CodeLink 12-slide shaker tray. The hybridization ports were sealed with 1 cm sealing strips (Amersham Biosciences, Piscataway, NJ), and the shaker tray(s) containing the slides was loaded into a New Brunswick Innova 4080 shaking incubator, with the hybridization chambers facing up. Slides were incubated for 20 hr at 37oC, while shaking at 300 rpm. The 12-slide shaker tray was removed from the shaker, and the hybridization chamber removed from each slide. Each slide was placed into the BioArray Rack of the Parallel Processing Tool (Amersham Biosciences, Piscataway, NJ) and incubated with 0.75x TNT (0.075 M Tris-HCl, pH7.6, 0.1125 M NaCl, 0.0375 % Tween-20) at 46oC for 1hr. The BioArray Rack was moved from the TNT containing reservoir to the small reagent reservoir containing 1:500 dilution of streptavidin-Alexa 647 (Molecular Probes, Eugene, OR). The signal was developed for 30 min at room temperature, before the reaction was stopped and slides were washed four times for 5 min each in TNT buffer (0.1 M Tris-HCl, pH7.6, 0.15 M NaCl, 0.05% Tween-20) using a large reagent reservoir. The slides were rinsed in ddH2O with 0.05% Tween-20 twice for 5 sec each before they were dried by centrifugation with a Qiagen Sigma 4-15C centrifuge (Valencia, CA) using a swinging bucket rotor (2x96) for exactly 3 min at 2000rpm (acceleration at position 9 and deceleration at position 9). The dried slides were stored in light protective slide boxes at room temperature prior to scanning.

scan_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The Axon GenePix Scanner (Axon Instrument, Union City, CA) was calibrated using the Calibration Slide supplied by Axon Instrument with GenePix 4.0 at 635 nm using the Calibration System. After calibration of the scanner, all processed slides were scanned with the laser set to 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10 microns. For consistency all slides were scanned the same day of color development, within an hour after dry spinning them and the data was analyzed using the CodeLink Expression Analysis Software version 2.2.25 (Amersham Biosciences, Piscataway, NJ).

data_processing: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44, supplemental methods.  Prior to statistical computation, the spot reading data was normalized. For this purpose a new nonlinear normalization procedure, similar to the centralization approach reported in the literature (Zien et al., 2001) was developed for the CodeLink array platform. The normalization procedure uses proprietary algorithm that assumes that in general, for an array with many probes, the majority of the signal represents genes that have unchanged expressions compared to controls, with the extreme values representing the true biology of the process and not some artifact due to measurement noise. The algorithm does not make the assumption that the true mRNA abundance being measured is linearly proportional to the spot reading signal or any assumption about the error distribution of such signals or their differential. Rather, the assumption of unchanged signals representing the bulk of the signal measurements is used to center a nonlinear curve fit to a reference template. This reference template is constructed for a large set of time matched, same tissue and same vehicle, control arrays, computing a median log signal for each probe. The replicate size of this set is adequate to ensure very small random error in the ensemble signal level for each reference probe. The curve fit corrects for some array processing problems, such as partial signal saturation, and improves the overall quality of the data compared to simple linear normalization methods. Essentially the curve tracks the mode of the signal distribution for sets of genes against the expected value for that set.

organism: Rattus norvegicus

source_name: LIVER, LIPOPOLYSACCHARIDE E. COLI O55:B5, 1.25mg/kg, 1 days

label_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The methods used for cRNA preparation (cDNA synthesis, cRNA preparation, and cRNA purification) are essentially as described in the CodeLink™ manual v2.1 as supplied by Amersham Biosciences (Piscataway, NJ) using the Qiagen BioRobot 9604 (Valencia, CA). cDNA synthesis, cRNA preparation, and cRNA purification were completely processed in a 96-well format using the automated Qiagen BioRobot 9604 procedure. 0.6 – 20 ìg of enriched RNA from different tissue sources were added to a reaction mixture in a final volume of 12 ìl, containing bacterial control RNA (1.5pg FixA, 5pgYjeK, 5pg AraB, 15pg EntF, 50pg FixB, 150pg HisB, 500pg LeuB, 1500pg gnd) and 1.0 ìl of 100 pmol ìl-1 T7-(dT)24 oligonucleotide primer (Proligo, Boulder, CO). The T7-(dT)24 oligonucleotide primer used, is an HPLC purified 63-mer with the sequence : 5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3'. The mixture was incubated for 10 min at 70oC and chilled on ice. On ice, 4 ul of 5x first-strand buffer, 2 ul 0.1 M DTT, 1 ul of 10 mM dNTP mix and 1 ul Superscript™II RNaseH-reverse transcriptase (200 U/ul) were added to the mixture to make a final volume of 20 ul. The mixture was incubated for 1 hr at 37oC. Second-strand cDNA was synthesized in a volume of 150 ul, containing 92 ul nuclease-free water, 30 ul of 5x second-strand buffer, 3 ul of 10 mM dNTP mix, 4 ul of Escherichia coli DNA polymerase I (10 U/ìl) and 1 ul of RNase H (2 U/ul) for 2 hr at 16oC. The cDNA was purified using a Qiagen QIAquick purification kit, and completely dried down using a Speed-Vac concentrator (45oC) for 2 hr. The dried product was resuspended in IVT reaction mix containing 3.0 ul of nuclease-free water, 4.0 ul 10x reaction buffer, 4.0 ul 75 mM ATP, 4.0 ul 75 mM GTP, 3.0 ul 75 mM CTP, 3.0 ul 75 mM UTP, 7.5 ul 10 mM Biotin 11-CTP, 7.5 ul 10 mM Biotin 11-UTP and 4.0 ul enzyme mix. The reaction mix was incubated for 14 hr at 37oC using an MJ Research 96-well PTC-200 Thermal Cycler (MJ Research, Waltham, MA), before the cRNA was purified using a Qiagen RNeasy® kit. The resulting cRNA yield was quantified using the 96-well ìQuan Universal Microplate Spectrophotometer Model MQX200 (BIO-TEK Instruments Inc., Winooski, VT) at a wavelength of 260 nm. Conformance of the cRNA sample to historical size distributions (the bulk of the cRNA product should be between 500 and 3,000 bases in size) was confirmed using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). Samples not near the historical norm were reprocessed starting from tissue or RNA.

growth_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Sprague-Dawley (Crl:CD®(SD)|GS BR) rats (aged 6-8 weeks and weighing 200 - 260 g), were purchased from Charles River Laboratories (Wilmington, MA). They were housed in plastic cages for 1 week for acclimation to the laboratory environment of a ventilated room (temperature, 22oC ±3oC; humidity, 30 - 70%; light/dark cycle, 12 h d-1, 6:00am - 6:00pm) until use. Certified Rodent Diet #5002 (PMI Feeds Inc.) and chlorinated tap water was available ad libitum.

extract_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. Following sacrifice, 6 mm disposable biopsy punches (#REF 33-36 Miltex, Inc. Bethpage, NY) were used to obtain tissue samples of approximately 100 mg. Samples were placed in cryogenic tubes and snap frozen. Poly A(+)-RNA from tissue samples was isolated using the MagNA Pure LC robot (Roche, Basel, Switzerland) in combination with the MagNA Pure LC mRNA Isolation kit I and II (Roche, Basel, Switzerland) for cells (see supplemental methods section) and tissues, respectively. Tissue samples were completely homogenized directly from ~100 mg punches stored on dry ice prior to application of lysis buffer to a final concentration of 65 mg tissue per ml of buffer. After complete homogenization, using disposable Omni Tip Disposable Generator Probes (Omni Inc, Warrenton, VA) and before loading of the samples into the 32-well MagNA Pure plate, the samples were drawn up 5-6 times through a 20-gauge needle attached to a 3-ml syringe to ensure any tissue pieces or clumps were removed from the lysate prior to robotic processing. Tissue sample processing was performed in duplicate wells (loading 150 ul of homogenized sample to each well) of the MagNA Pure LC, which is programmed to extract mRNA using the oligo-dT selection method into a final elution volume of 100 ul. Poly A(+) RNA sample concentration was performed manually using a standard ethanol precipitation protocol in the presence of glycogen (50 ug/ml). After precipitation the final purified RNA sample was resuspended in 7 ìl DEPC-H2O and quantified using a Ribogreen high-range assay (Molecular Probes) on the Wallac Victor2 Fluorometer (Perkin-Elmer, Fremont, CA). Additionally, the integrity of each RNA sample was determined, by comparison to historical standards (no gross degradation should be visible as suggested by clear 18S and 28S peaks on top of a hump of complex RNA, with lower amounts of RNA below 18S than under and above the 18S peak), using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) in combination with the RNA 6000 Nano Lab Chip kit (Agilent Technologies).

treatment_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Compounds were administered via the route of administration (ROA) that corresponds to that by which humans receive the drug. Compounds were typically administered orally (PO) (83%), intravenously (IV) (9.4%), subcutaneously (SC) (5.7%), or intraperitoneally (IP) (2%). If the compound is a toxicant or a biochemical standard, it was administered orally. For oral dosing, the vehicle choice largely depends on the solubility of the compound in water. Water-soluble compounds were administered in water. Insoluble compounds are administered in either corn oil or 0.5% carboxymethylcellulose (CMC) using the best literature recommendation as a guide. IV administered compounds were usually dissolved in saline and SC administered compounds in corn oil. The highest dose the rats receive is the Maximum Tolerated Dose (MTD). The dosing of animals was staggered based on intended harvest order to ensure that sacrifice occurred within 30 minutes of the recorded time point. Dosing frequency was as described in Sample_characteristics for the particular treatment.

tag: Sprague-Dawley

value: 6 to 8 weeks

tag: sex

tag: tissue

value: LIVER

tag: treatment compound

value: LIPOPOLYSACCHARIDE E. COLI O55:B5

tag: dose

tag: solvent

value: SALINE

tag: administration route

value: INTRAVENOUS

tag: frequency of dosing

value: DAILY

tag: treatment duration

value: 1 days

tag: experiment date


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 3days exp4536 rep2 19921

description:
HybID: 19921
treated sample for experiment (RepID) 4536
replicate 2 of 2
Experimental sample
Replicate experimental sample: GSM222688: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_3days_exp4536_rep1_19920
Matched control sample: GSM204608: LIVER_vehicle_NA_.25days_control_NA_18857
Matched control sample: GSM204708: LIVER_vehicle_NA_1days_control_NA_18859
Matched control sample: GSM204742: LIVER_vehicle_NA_3days_control_NA_18863
Matched control sample: GSM204602: LIVER_vehicle_NA_.25days_control_NA_18865
Matched control sample: GSM204691: LIVER_vehicle_NA_1days_control_NA_18868
Matched control sample: GSM204760: LIVER_vehicle_NA_3days_control_NA_18872
Matched control sample: GSM204663: LIVER_vehicle_NA_1days_control_NA_18986
Matched control sample: GSM204604: LIVER_vehicle_NA_.25days_control_NA_19233
Matched control sample: GSM204677: LIVER_vehicle_NA_1days_control_NA_19236
Matched control sample: GSM204771: LIVER_vehicle_NA_3days_control_NA_19238
Matched control sample: GSM204642: LIVER_vehicle_NA_1days_control_NA_80157
Matched control sample: GSM204718: LIVER_vehicle_NA_1days_control_NA_80159
Matched control sample: GSM204621: LIVER_vehicle_NA_.25days_control_NA_80565
Matched control sample: GSM204768: LIVER_vehicle_NA_3days_control_NA_80570
Matched control sample: GSM204868: LIVER_vehicle_NA_5days_control_NA_80573
Matched control sample: GSM204669: LIVER_vehicle_NA_1days_control_NA_80683
Matched control sample: GSM204629: LIVER_vehicle_NA_.25days_control_NA_81664
Matched control sample: GSM204782: LIVER_vehicle_NA_3days_control_NA_81665
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, LIPOPOLYSACCHARIDE E. COLI O55:B5, 1.25mg/kg, 3 days

tag: age

value: 3 days


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 3days exp6542 rep1 87348

description:
HybID: 87348
treated sample for experiment (RepID) 6542
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM222691: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_3days_exp6542_rep2_87346
Replicate experimental sample: GSM222692: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_3days_exp6542_rep3_87347
Matched control sample: GSM204657: LIVER_vehicle_NA_1days_control_NA_87149
Matched control sample: GSM204719: LIVER_vehicle_NA_1days_control_NA_87150
Matched control sample: GSM204697: LIVER_vehicle_NA_1days_control_NA_87151
Matched control sample: GSM204759: LIVER_vehicle_NA_3days_control_NA_87152
Matched control sample: GSM204796: LIVER_vehicle_NA_3days_control_NA_87153
Matched control sample: GSM204785: LIVER_vehicle_NA_3days_control_NA_87154
Matched control sample: GSM204871: LIVER_vehicle_NA_5days_control_NA_87155
Matched control sample: GSM204839: LIVER_vehicle_NA_5days_control_NA_87156
Matched control sample: GSM204861: LIVER_vehicle_NA_5days_control_NA_87215
Matched control sample: GSM204714: LIVER_vehicle_NA_1days_control_NA_87337
Matched control sample: GSM204637: LIVER_vehicle_NA_1days_control_NA_87338
Matched control sample: GSM204689: LIVER_vehicle_NA_1days_control_NA_87339
Matched control sample: GSM204793: LIVER_vehicle_NA_3days_control_NA_87340
Matched control sample: GSM204753: LIVER_vehicle_NA_3days_control_NA_87341
Matched control sample: GSM204778: LIVER_vehicle_NA_3days_control_NA_87342
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 3days exp6542 rep2 87346

description:
HybID: 87346
treated sample for experiment (RepID) 6542
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM222692: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_3days_exp6542_rep3_87347
Replicate experimental sample: GSM222690: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_3days_exp6542_rep1_87348
Matched control sample: GSM204657: LIVER_vehicle_NA_1days_control_NA_87149
Matched control sample: GSM204719: LIVER_vehicle_NA_1days_control_NA_87150
Matched control sample: GSM204697: LIVER_vehicle_NA_1days_control_NA_87151
Matched control sample: GSM204759: LIVER_vehicle_NA_3days_control_NA_87152
Matched control sample: GSM204796: LIVER_vehicle_NA_3days_control_NA_87153
Matched control sample: GSM204785: LIVER_vehicle_NA_3days_control_NA_87154
Matched control sample: GSM204871: LIVER_vehicle_NA_5days_control_NA_87155
Matched control sample: GSM204839: LIVER_vehicle_NA_5days_control_NA_87156
Matched control sample: GSM204861: LIVER_vehicle_NA_5days_control_NA_87215
Matched control sample: GSM204714: LIVER_vehicle_NA_1days_control_NA_87337
Matched control sample: GSM204637: LIVER_vehicle_NA_1days_control_NA_87338
Matched control sample: GSM204689: LIVER_vehicle_NA_1days_control_NA_87339
Matched control sample: GSM204793: LIVER_vehicle_NA_3days_control_NA_87340
Matched control sample: GSM204753: LIVER_vehicle_NA_3days_control_NA_87341
Matched control sample: GSM204778: LIVER_vehicle_NA_3days_control_NA_87342
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 3days exp6542 rep3 87347

description:
HybID: 87347
treated sample for experiment (RepID) 6542
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM222691: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_3days_exp6542_rep2_87346
Replicate experimental sample: GSM222690: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_3days_exp6542_rep1_87348
Matched control sample: GSM204657: LIVER_vehicle_NA_1days_control_NA_87149
Matched control sample: GSM204719: LIVER_vehicle_NA_1days_control_NA_87150
Matched control sample: GSM204697: LIVER_vehicle_NA_1days_control_NA_87151
Matched control sample: GSM204759: LIVER_vehicle_NA_3days_control_NA_87152
Matched control sample: GSM204796: LIVER_vehicle_NA_3days_control_NA_87153
Matched control sample: GSM204785: LIVER_vehicle_NA_3days_control_NA_87154
Matched control sample: GSM204871: LIVER_vehicle_NA_5days_control_NA_87155
Matched control sample: GSM204839: LIVER_vehicle_NA_5days_control_NA_87156
Matched control sample: GSM204861: LIVER_vehicle_NA_5days_control_NA_87215
Matched control sample: GSM204714: LIVER_vehicle_NA_1days_control_NA_87337
Matched control sample: GSM204637: LIVER_vehicle_NA_1days_control_NA_87338
Matched control sample: GSM204689: LIVER_vehicle_NA_1days_control_NA_87339
Matched control sample: GSM204793: LIVER_vehicle_NA_3days_control_NA_87340
Matched control sample: GSM204753: LIVER_vehicle_NA_3days_control_NA_87341
Matched control sample: GSM204778: LIVER_vehicle_NA_3days_control_NA_87342
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 3days exp4536 rep1 19920

description:
HybID: 19920
treated sample for experiment (RepID) 4536
replicate 1 of 2
Experimental sample
Replicate experimental sample: GSM222689: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_3days_exp4536_rep2_19921
Matched control sample: GSM204608: LIVER_vehicle_NA_.25days_control_NA_18857
Matched control sample: GSM204708: LIVER_vehicle_NA_1days_control_NA_18859
Matched control sample: GSM204742: LIVER_vehicle_NA_3days_control_NA_18863
Matched control sample: GSM204602: LIVER_vehicle_NA_.25days_control_NA_18865
Matched control sample: GSM204691: LIVER_vehicle_NA_1days_control_NA_18868
Matched control sample: GSM204760: LIVER_vehicle_NA_3days_control_NA_18872
Matched control sample: GSM204663: LIVER_vehicle_NA_1days_control_NA_18986
Matched control sample: GSM204604: LIVER_vehicle_NA_.25days_control_NA_19233
Matched control sample: GSM204677: LIVER_vehicle_NA_1days_control_NA_19236
Matched control sample: GSM204771: LIVER_vehicle_NA_3days_control_NA_19238
Matched control sample: GSM204642: LIVER_vehicle_NA_1days_control_NA_80157
Matched control sample: GSM204718: LIVER_vehicle_NA_1days_control_NA_80159
Matched control sample: GSM204621: LIVER_vehicle_NA_.25days_control_NA_80565
Matched control sample: GSM204768: LIVER_vehicle_NA_3days_control_NA_80570
Matched control sample: GSM204868: LIVER_vehicle_NA_5days_control_NA_80573
Matched control sample: GSM204669: LIVER_vehicle_NA_1days_control_NA_80683
Matched control sample: GSM204629: LIVER_vehicle_NA_.25days_control_NA_81664
Matched control sample: GSM204782: LIVER_vehicle_NA_3days_control_NA_81665
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 1days exp6547 rep1 87343

description:
HybID: 87343
treated sample for experiment (RepID) 6547
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM222686: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_1days_exp6547_rep2_87344
Replicate experimental sample: GSM222687: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_1days_exp6547_rep3_87345
Matched control sample: GSM204657: LIVER_vehicle_NA_1days_control_NA_87149
Matched control sample: GSM204719: LIVER_vehicle_NA_1days_control_NA_87150
Matched control sample: GSM204697: LIVER_vehicle_NA_1days_control_NA_87151
Matched control sample: GSM204759: LIVER_vehicle_NA_3days_control_NA_87152
Matched control sample: GSM204796: LIVER_vehicle_NA_3days_control_NA_87153
Matched control sample: GSM204785: LIVER_vehicle_NA_3days_control_NA_87154
Matched control sample: GSM204871: LIVER_vehicle_NA_5days_control_NA_87155
Matched control sample: GSM204839: LIVER_vehicle_NA_5days_control_NA_87156
Matched control sample: GSM204861: LIVER_vehicle_NA_5days_control_NA_87215
Matched control sample: GSM204714: LIVER_vehicle_NA_1days_control_NA_87337
Matched control sample: GSM204637: LIVER_vehicle_NA_1days_control_NA_87338
Matched control sample: GSM204689: LIVER_vehicle_NA_1days_control_NA_87339
Matched control sample: GSM204793: LIVER_vehicle_NA_3days_control_NA_87340
Matched control sample: GSM204753: LIVER_vehicle_NA_3days_control_NA_87341
Matched control sample: GSM204778: LIVER_vehicle_NA_3days_control_NA_87342
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 1days exp4548 rep1 81507

description:
HybID: 81507
treated sample for experiment (RepID) 4548
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM222683: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_1days_exp4548_rep2_19917
Replicate experimental sample: GSM222684: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_1days_exp4548_rep3_19918
Matched control sample: GSM204608: LIVER_vehicle_NA_.25days_control_NA_18857
Matched control sample: GSM204708: LIVER_vehicle_NA_1days_control_NA_18859
Matched control sample: GSM204742: LIVER_vehicle_NA_3days_control_NA_18863
Matched control sample: GSM204602: LIVER_vehicle_NA_.25days_control_NA_18865
Matched control sample: GSM204691: LIVER_vehicle_NA_1days_control_NA_18868
Matched control sample: GSM204760: LIVER_vehicle_NA_3days_control_NA_18872
Matched control sample: GSM204663: LIVER_vehicle_NA_1days_control_NA_18986
Matched control sample: GSM204604: LIVER_vehicle_NA_.25days_control_NA_19233
Matched control sample: GSM204677: LIVER_vehicle_NA_1days_control_NA_19236
Matched control sample: GSM204771: LIVER_vehicle_NA_3days_control_NA_19238
Matched control sample: GSM204642: LIVER_vehicle_NA_1days_control_NA_80157
Matched control sample: GSM204718: LIVER_vehicle_NA_1days_control_NA_80159
Matched control sample: GSM204621: LIVER_vehicle_NA_.25days_control_NA_80565
Matched control sample: GSM204768: LIVER_vehicle_NA_3days_control_NA_80570
Matched control sample: GSM204868: LIVER_vehicle_NA_5days_control_NA_80573
Matched control sample: GSM204669: LIVER_vehicle_NA_1days_control_NA_80683
Matched control sample: GSM204629: LIVER_vehicle_NA_.25days_control_NA_81664
Matched control sample: GSM204782: LIVER_vehicle_NA_3days_control_NA_81665
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 1days exp4548 rep2 19917

description:
HybID: 19917
treated sample for experiment (RepID) 4548
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM222684: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_1days_exp4548_rep3_19918
Replicate experimental sample: GSM222682: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_1days_exp4548_rep1_81507
Matched control sample: GSM204608: LIVER_vehicle_NA_.25days_control_NA_18857
Matched control sample: GSM204708: LIVER_vehicle_NA_1days_control_NA_18859
Matched control sample: GSM204742: LIVER_vehicle_NA_3days_control_NA_18863
Matched control sample: GSM204602: LIVER_vehicle_NA_.25days_control_NA_18865
Matched control sample: GSM204691: LIVER_vehicle_NA_1days_control_NA_18868
Matched control sample: GSM204760: LIVER_vehicle_NA_3days_control_NA_18872
Matched control sample: GSM204663: LIVER_vehicle_NA_1days_control_NA_18986
Matched control sample: GSM204604: LIVER_vehicle_NA_.25days_control_NA_19233
Matched control sample: GSM204677: LIVER_vehicle_NA_1days_control_NA_19236
Matched control sample: GSM204771: LIVER_vehicle_NA_3days_control_NA_19238
Matched control sample: GSM204642: LIVER_vehicle_NA_1days_control_NA_80157
Matched control sample: GSM204718: LIVER_vehicle_NA_1days_control_NA_80159
Matched control sample: GSM204621: LIVER_vehicle_NA_.25days_control_NA_80565
Matched control sample: GSM204768: LIVER_vehicle_NA_3days_control_NA_80570
Matched control sample: GSM204868: LIVER_vehicle_NA_5days_control_NA_80573
Matched control sample: GSM204669: LIVER_vehicle_NA_1days_control_NA_80683
Matched control sample: GSM204629: LIVER_vehicle_NA_.25days_control_NA_81664
Matched control sample: GSM204782: LIVER_vehicle_NA_3days_control_NA_81665
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg .25days exp4519 rep2 19916

description:
HybID: 19916
treated sample for experiment (RepID) 4519
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM222679: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_.25days_exp4519_rep1_81300
Replicate experimental sample: GSM222681: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_.25days_exp4519_rep3_81425
Matched control sample: GSM204608: LIVER_vehicle_NA_.25days_control_NA_18857
Matched control sample: GSM204708: LIVER_vehicle_NA_1days_control_NA_18859
Matched control sample: GSM204742: LIVER_vehicle_NA_3days_control_NA_18863
Matched control sample: GSM204602: LIVER_vehicle_NA_.25days_control_NA_18865
Matched control sample: GSM204691: LIVER_vehicle_NA_1days_control_NA_18868
Matched control sample: GSM204760: LIVER_vehicle_NA_3days_control_NA_18872
Matched control sample: GSM204663: LIVER_vehicle_NA_1days_control_NA_18986
Matched control sample: GSM204604: LIVER_vehicle_NA_.25days_control_NA_19233
Matched control sample: GSM204677: LIVER_vehicle_NA_1days_control_NA_19236
Matched control sample: GSM204771: LIVER_vehicle_NA_3days_control_NA_19238
Matched control sample: GSM204642: LIVER_vehicle_NA_1days_control_NA_80157
Matched control sample: GSM204718: LIVER_vehicle_NA_1days_control_NA_80159
Matched control sample: GSM204621: LIVER_vehicle_NA_.25days_control_NA_80565
Matched control sample: GSM204768: LIVER_vehicle_NA_3days_control_NA_80570
Matched control sample: GSM204868: LIVER_vehicle_NA_5days_control_NA_80573
Matched control sample: GSM204669: LIVER_vehicle_NA_1days_control_NA_80683
Matched control sample: GSM204629: LIVER_vehicle_NA_.25days_control_NA_81664
Matched control sample: GSM204782: LIVER_vehicle_NA_3days_control_NA_81665
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, LIPOPOLYSACCHARIDE E. COLI O55:B5, 1.25mg/kg, .25 days

value: .25 days


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 1days exp6547 rep2 87344

description:
HybID: 87344
treated sample for experiment (RepID) 6547
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM222685: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_1days_exp6547_rep1_87343
Replicate experimental sample: GSM222687: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_1days_exp6547_rep3_87345
Matched control sample: GSM204657: LIVER_vehicle_NA_1days_control_NA_87149
Matched control sample: GSM204719: LIVER_vehicle_NA_1days_control_NA_87150
Matched control sample: GSM204697: LIVER_vehicle_NA_1days_control_NA_87151
Matched control sample: GSM204759: LIVER_vehicle_NA_3days_control_NA_87152
Matched control sample: GSM204796: LIVER_vehicle_NA_3days_control_NA_87153
Matched control sample: GSM204785: LIVER_vehicle_NA_3days_control_NA_87154
Matched control sample: GSM204871: LIVER_vehicle_NA_5days_control_NA_87155
Matched control sample: GSM204839: LIVER_vehicle_NA_5days_control_NA_87156
Matched control sample: GSM204861: LIVER_vehicle_NA_5days_control_NA_87215
Matched control sample: GSM204714: LIVER_vehicle_NA_1days_control_NA_87337
Matched control sample: GSM204637: LIVER_vehicle_NA_1days_control_NA_87338
Matched control sample: GSM204689: LIVER_vehicle_NA_1days_control_NA_87339
Matched control sample: GSM204793: LIVER_vehicle_NA_3days_control_NA_87340
Matched control sample: GSM204753: LIVER_vehicle_NA_3days_control_NA_87341
Matched control sample: GSM204778: LIVER_vehicle_NA_3days_control_NA_87342
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg .25days exp4519 rep1 81300

description:
HybID: 81300
treated sample for experiment (RepID) 4519
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM222680: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_.25days_exp4519_rep2_19916
Replicate experimental sample: GSM222681: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_.25days_exp4519_rep3_81425
Matched control sample: GSM204608: LIVER_vehicle_NA_.25days_control_NA_18857
Matched control sample: GSM204708: LIVER_vehicle_NA_1days_control_NA_18859
Matched control sample: GSM204742: LIVER_vehicle_NA_3days_control_NA_18863
Matched control sample: GSM204602: LIVER_vehicle_NA_.25days_control_NA_18865
Matched control sample: GSM204691: LIVER_vehicle_NA_1days_control_NA_18868
Matched control sample: GSM204760: LIVER_vehicle_NA_3days_control_NA_18872
Matched control sample: GSM204663: LIVER_vehicle_NA_1days_control_NA_18986
Matched control sample: GSM204604: LIVER_vehicle_NA_.25days_control_NA_19233
Matched control sample: GSM204677: LIVER_vehicle_NA_1days_control_NA_19236
Matched control sample: GSM204771: LIVER_vehicle_NA_3days_control_NA_19238
Matched control sample: GSM204642: LIVER_vehicle_NA_1days_control_NA_80157
Matched control sample: GSM204718: LIVER_vehicle_NA_1days_control_NA_80159
Matched control sample: GSM204621: LIVER_vehicle_NA_.25days_control_NA_80565
Matched control sample: GSM204768: LIVER_vehicle_NA_3days_control_NA_80570
Matched control sample: GSM204868: LIVER_vehicle_NA_5days_control_NA_80573
Matched control sample: GSM204669: LIVER_vehicle_NA_1days_control_NA_80683
Matched control sample: GSM204629: LIVER_vehicle_NA_.25days_control_NA_81664
Matched control sample: GSM204782: LIVER_vehicle_NA_3days_control_NA_81665
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: EAC tumor biopsy from 40331

status: Public on Jun 01 2008

type: genomic

city: Herston

first: Derek

middle: John

last: Nancarrow

state: Queensland

address: 300 Herston Road

department: Genetics & Population Health

country: Australia

institute: Queensland Institute of Medical Research

description: The EAC biopsies used in this study were collected as part of the Australian Cancer Study.

hyb_protocol: The dried precipitated pellet was then resuspended in WG-RA1 and hybridized to a beadchip along with WG-RA1 and formamide. The arrays were then incubated overnight at 48°C, after which they underwent single-base extension on a Teflow chamber rack system (Tecan, Männedorf, Switzerland) using WG-XC1, WG-XC2, and WG-TEM.

scan_protocol: After the single-base extension step, the beadchips were stained with WG-LTM and WG-ATM, dried for 1 h, then imaged using a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Beadstudio 2.0 (Illumina). EAC samples log_R_ratio values were generated using the squamous sample 192R as a reference. All genomic positions were based upon hg17 from the UCSC Genome Browser.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Esopageal Adenocarcinoma Tumor Biopsy

label_protocol: The Infinium II assay was done using Illumina Sentrix HumanHap300 genotyping BeadChip arrays (317K, TagSNP Phase I, v1.1) according to the manufacturer's specifications (Illumina, San Diego, CA). Briefly, 750 ng of genomic DNA were amplified at 37°C overnight, using solutions WG-AMM and WG-MP1. After overnight incubation, the amplified DNA was fragmented using WG-FRG and precipitated with isopropanol after the addition of WG-PA1.

extract_protocol: As per QIAGEN tissue lyser protocol using ALLPREP Kit

treatment_protocol: Fresh tissue was placed directly into RNAlater solution, stored at 4°C overnight, then -20°C. Long-term storage was then at -80°C after access RNAlater was removed.

tag: Biopsy taken by endoscopy prior to treatment. Subject details

tag: Gender

tag: Age

value: 65 years

tag: Tissue

value: EAC tumor

tag: Tumor stage

value: III