title: Gill_28C_steadyacclim_rep6


title: Gill_19C_steadyacclim_rep4

status: Public on Jul 15 2010

type: RNA

city: Pacific Grove

first: Cheryl

middle: A

last: Logan

state: CA

address: 120 Ocean View Blvd

country: USA

institute: Stanford University

hyb_protocol: Hybridizations were conducted overnight at 65°C in Genetix (Boston, MA, USA) humid hybridization chambers. After hybridization, slides were washed by repeated vigorous immersion in 0.5x SSC and 0.01% SDS for 2 min to remove unbound dye. Slides were then washed in 0.6x SSC on a shaker for 15 min and dried by centrifugation.

scan_protocol: The slides were scanned on an AXON GenePix 4000B microarray scanner in GenePix 4.0 (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA).

data_processing: Raw data for each gene (median pixel intensity of each spot with background correction) were imported from GenePix 4.0 into GeneSpring version 7.3 (Silicon Genetics, Redwood, CA, USA) for subsequent analysis. We normalized the data using intensity-dependent locally weighted linear regression (lowess) transformation to correct for spatial variation in the array due to inconsistencies in printing pins, slide surface variability, and differences in local hybridization conditions across a slide. We normalized and filtered our data in Genespring 7.3. To obtain a set of reliable genes from the normalized data, we discarded all probes that were flagged as irregular by Genepix 4.0 software or by hand (irregularities are generally due to specks of dust or scratches on slides) and genes that showed standard deviations of >1.4. All subsequent analyses were performed on this filtered list comprising 7,488 probes.

molecule: total RNA

organism: Gillichthys mirabilis

source_name: Gillichthys mirabilis, gill tissues, 19C acclim,1 month

label_protocol: Single stranded cDNA was labeled with either Cy3 (reference samples) or Cy5 (acclimation samples) cyanine monoreactive dye (Amersham, Piscataway, NJ, USA), prepared in 80 µl of dimethylsulfoxide.

extract_protocol: Total RNA was extracted from gill tissue using the Qiagen Tissuelyser for homogenization and the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).  Total RNA was determined by A260 absorbance using a Nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE, USA).  Samples were run on 1% agarose gels to confirm RNA integrity. 15 µg of total RNA from each sample were reverse transcribed with 3 µl of AffinityScript enzyme (Agilent Technologies, Santa Clara, CA, USA), 0.75 µl oligo(dT15) and 0.75 µl pdN9 random hexamer primers, and amino-allyl modified dNTPs. RNA templates were removed from the RT reactions by incubation at 65°C for 30 min in 0.2 mol l-1 NaOH and 0.1 mol l-1 EDTA. cDNA was precipitated at -80°C for 20 min in 4.5 µl 3M sodium acetate and 2.5 volumes on 100% ethanol. Samples were centrifuged at 10,000 rpm for 20 min at 4°C and resuspended in 8 µl of nuclease free water and 2 µl of fresh 0.5 M sodium bicarbonate.

tag: temperature

tag: tissue type

value: Gill tissue

source_name: Gillichthys mirabilis, gill tissue, flow-through seawater tank (~13C), pooled total RNA for reference

tag: reference


title: Gill_9C_steadyacclim_rep8

source_name: Gillichthys mirabilis, gill tissues, 9C acclim,1 month

value: flow-through seawater tank (~13C), pooled total RNA


title: Gill_19C_steadyacclim_rep2


title: Gill_9C_steadyacclim_rep7


title: Gill_28C_steadyacclim_rep1

source_name: Gillichthys mirabilis, gill tissues, 28C acclim,1 month


title: Gill_28C_steadyacclim_rep2


title: Gill_9C_steadyacclim_rep4


title: Gill_9C_steadyacclim_rep6


title: Gill_9C_steadyacclim_rep1


title: Gill_19C_steadyacclim_rep1


title: Gill_9C_steadyacclim_rep2


title: Gill_9C_steadyacclim_rep3


title: 6.5% ethanol replicate 2/mutant CM1

status: Public on Jul 01 2010

city: East Geelong

first: Dragana

last: Stanley

state: Victoria

address: 5 Portarlington Rd

department: AAHL

country: Australia

institute: CSIRO

description: normal dye direction (sample red, pool green)

hyb_protocol: Quigene purified labeled samples were resuspended in Hybing solution containing 10 mg ml-1 of yeast tRNA and 10 mg ml-1 of Samon sperm DNA in Dig Easy Hyb solution (Roche)

scan_protocol: GenePix-Pro 4000B

data_processing: GenowizTM 4.0.2.1 software (Ocimum Biosolutions). Log 2 transformed ratios (AlexaFluor 647/AlexaFluor 555), Lowess normalised with minimum and maximum fold set to -100 and 100 respectively.

label: AlexaFluor 647

organism: Saccharomyces cerevisiae

source_name: Total RNA from second culture of mutant CM1 grown at 6.5% ethanol

label_protocol: Invitrogen “SuperScript TM Plus Indirect cDNA Labeling Module” (#L1014-04) was used for both cDNA synthesis and labelling with the AlexaFluor (AF647/AF555) dyes that were also supplied in the kit.

extract_protocol: RNA was extracted from equal numbers of yeast cells using the glass bead extraction method, essentially as described by Collart and Oliviero (1997), followed by DNase treatment using the Ambion DNA-FreeTM

treatment_protocol: Inoculum from unstressed late exponentioal culture of each strain was added to 3 separate cultures containing 0% ethanol and to other 3 cultures containing 6.5% ethanol.

tag: cell type

value: ethanol stressed culture 2

tag: genotype/variation

value: mutant CM1

label: AlexaFluor 555

source_name: Total RNA made by pooling Total RNA extracted from 3 cultures of W303-1A grown at 0% ethanol

value: 0% ethanol reference pool


title: 6.5% ethanol replicate 3/mutant CM1

source_name: Total RNA from third culture of mutant CM1 grown at 6.5% ethanol

value: ethanol stressed culture 3


title: 0% ethanol replicate 3/mutant CM1

source_name: Total RNA from third culture of mutant CM1 grown at 0% ethanol

value: non stressed culture 3


title: 6.5% ethanol replicate 1/mutant CM1

description: dye swapped experiment with pool labeled red

source_name: Total RNA from first culture of mutant CM1 grown at 6.5% ethanol

value: ethanol stressed culture 1


title: 6.5% ethanol replicate 2/mutant SM1

source_name: Total RNA from second culture of mutant SM1 grown at 6.5% ethanol

value: mutant SM1


title: 6.5% ethanol replicate 3/mutant SM1

source_name: Total RNA from third culture of mutant SM1 grown at 6.5% ethanol


title: 0% ethanol replicate 3/mutant SM1

source_name: Total RNA from third culture of mutant SM1 grown at 0% ethanol


title: 6.5% ethanol replicate 3/W303-1A

source_name: Total RNA from third culture of W303-1A grown at 6.5% ethanol


title: 0% ethanol replicate 1/mutant CM1

source_name: Total RNA from first culture of mutant CM1 grown at 0% ethanol

value: non stressed culture 1


title: 6.5% ethanol replicate 1/mutant SM1

source_name: Total RNA from first culture of mutant SM1 grown at 6.5% ethanol


title: 0% ethanol replicate 3/W303-1A

source_name: Total RNA from third culture of W303-1A grown at 0% ethanol


title: 0% ethanol replicate 1/W303-1A

source_name: Total RNA from first culture grown at 0% ethanol


title: 0% ethanol replicate 1/mutant SM1

source_name: Total RNA from first culture of mutant SM1 grown at 0% ethanol


title: 0% ethanol replicate 2/mutant SM1

source_name: Total RNA from second culture of mutant SM1 grown at 0% ethanol

value: non stressed culture 2


title: 6.5% ethanol replicate 1/W303-1A

source_name: Total RNA from first culture grown at 6.5% ethanol


title: 6.5% ethanol replicate 2/W303-1A

source_name: Total RNA from second culture of W303-1A grown at 6.5% ethanol


title: 0% ethanol replicate 2/W303-1A

source_name: Total RNA from second culture of W303-1A grown at 0% ethanol


title: B6.D2(Tryp1-Gpnmb-)/SJ, biological replicate 3

city: Iowa City

first: Markus

middle: H

last: Kuehn

state: IA

address: 375 Newton Road

department: Ophthalmology and Visual Sciences

institute: University of Iowa

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

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

data_processing: Data from cell files were normalized using RMAExpress software, using background adjust, quantile normalization and PLM summarization

label: biotin

organism: Mus musculus

source_name: 60 day old B6-D2 congenic iris

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Eyes were dissected in phosphate buffered saline and irides from 2 animals were pooled to form one sample

extract_protocol: Tissue was homogenized and total RNA was extracted using Aurum Total RNA Mini Kit (Bio-Rad Laboratories),  RNA was treated with DNase I and purified by EtOH preceipitation.

tag: age

value: 60 day old

tag: strain

tag: tissue

value: adult iris


title: B6.D2(Tryp1-Gpnmb-)/SJ, biological replicate 2


title: B6-(Cg)TyrC-2J, biological rep3

source_name: 60 day old B6-albino iris


title: B6-(Cg)TyrC-2J, biological rep2


title: B6-(Cg)TyrC-2J, biological rep1


title: B6.D2(Tryp1-Gpnmb-)/SJ, biological replicate 1


title: 0% ethanol replicate 2/mutant CM1

source_name: Total RNA from second culture of mutant CM1 grown at 0% ethanol

source_name: Total RNA made by pooling Total RNA extracted from 3 cultures of W303-1A grown at 0% ethanol


title: smoking alcoholic1

city: Brisbane

first: Traute

last: Flatscher-Bader

state: Queensland

address: The University of Queensland, Upland Road, QBI Building (79)

department: The Queensland Brain Institute

institute: The University of Queensland

description: the reference pool consisted of aliquots of the individual samples

hyb_protocol: To the concentrated cDNA, 16 lL 20· saline sodium citrate (SSC), 40 lL deionized formamide and 2 lL 20% (w/v) sodium dodecyl sulfate (SDS) were added. Samples were incubated at 95 C for 5 min, then at 45 C for 60 min, then chilled on ice. The cDNA microarrays were manufactured by the University Health Network (UHN) Microarray Centre at the Ontario Cancer Institute, Canada. Arrays were robotically printed on CMT-GAPS slides (Corning Inc., Acton, MA, USA). The Human 19K version 2.2 array contained 19200 I.M.A.G.E. Consortium clones spotted in duplicate over two slides. Clones were sequenced and verified by the UHN Microarray Centre. Published sequences are available at http://www.microarraysca/. each aRNA from on individal NA sample was hybridised competitively against a reference sample onto one array. The microarray slides were incubated overnight for 18 h at 42 C. Slides were washed in 1· SSC/0.1% (w/v) SDS,  0.5· SSC, 0.2· SSC, sequentially, at 50 C for 10 min, with gentle agitation and then centrifuged at 400 g for 5 min to remove residual wash solution.

scan_protocol: Slides were immediately scanned on a Genetic Microsystem scanner using GMS scan array software (Genetic Microsystem Inc, Woburn, MA, USA) at a resolution of 10nm. Spot detection on the scanned images was performed by auto-segmentation using the standard setting of the ImaGene 6.1 (Biodiscovery, El Segundo, CA, USA) software.

data_processing: GeneSpring 6.2 software (Silicon Genetics, Redwood City, California, USA) was used for data normalisation and analysis.  A per-spot and per-chip intensity-dependent Lowess fit normalization was carried out. Features other than those which were represented as ‘not flagged for irregular characteristics’ by the default settings of ImaGene 6.1 in least 18 of 20 hybridisations were filtered out.  The GeneSpring cross-gene error model was used to quantify the average constant error (ACE) across the arrays.  Only spots with a signal of the universal reference above ACE in one of the pathology groups were included.

organism: Homo sapiens

source_name: nucleus accumbens, alcoholic smoker

label_protocol: To 6 lg aRNA, 5 lg random primers were added in 20 lL with Rnase-free H2O. Samples were incubated at 70 C for 10 min, then chilled on ice. To each sample, 1.5 lL (300 U) Superscript II, 8 lL 5 · 1st strand buffer, 4 lL 100 mM DTT, 1 lL RNase inhibitor, 1 lL 25mM d(GAT)TP, 2 lL 2.5 mM dCTP, and either 2 lL FluoroLink Cy3-dCTP or 2 lL FluoroLink Cy5-dCTP (Amersham Biosciences, Sydney, New South Wales, Australia), were added. Samples were incubated at 42 C for 1 h. RNAwas hydrolysed by the addition of 1 lL 0.5 M EDTA (pH 8) and 2 lL 2 M NaOH, followed by incubation at 65 C for 10 min. Solutions were neutralized by the addition of 4 lL 1 M HCl, 4 lL 1 M Tris/HCl (pH 8) and 100 mM sodium acetate. cDNA samples were combined and purified though a QIAQuick PCR purification column (Qiagen, Melbourne, Victoria, Australia) according to the manufacturer’s instructions. To the eluent, 10 lL (10 lg) human Cot-1 DNA (GibcoBRL) were added and the volume reduced to 22 lL with a Microcon YM-30 filter (Millipore).

extract_protocol: RNA extraction and aRNA synthesis:Total RNA was extracted from 50 mg frozen tissue with 1 mL TRIzol (Invitrogen, Melbourne, Victoria, Australia) following the manufacturer’s instructions. Samples were suspended in RNAse/ DNAse-free water, maintaining concentrations above 1 lg/lL, then frozen at – 80 C. Anti-sense RNA (aRNA) was synthesised by linear amplification (Eberwine et al. 1992). Briefly, 1 lg total RNA with 1 lg T7-oligo dT21 primer (5'-TCTAGTCGACGGCCAGTGAATTGTAATACGACTCACTATAGGGCGT21-3') in 5 lL was incubated at 70 C for 4 min then chilled on ice. Next, 1 lL SuperScript II (200 U, GibcoBRL, Melbourne, Australia), 2 lL 100 mM dithiothreitol (DTT), 4 lL SuperScript II 1st strand buffer, 1 lL RNase inhibitor (40 U, GibcoBRL), 1 lL 10mM dNTPs (Sigma, Sydney, Australia) and 1 lL H2O were added. Samples were incubated at 42 C for 1 h then at 65 C for 15 min. To this, 1 lL ribonuclease H (2 U, Promega, Sydney, New South Wales, Australia), 1 lL Escherichia coli DNA ligase (5 U, New England Biolab, Brisbane, Queensland, Australia), 5 lL E. coli DNA polymerase I (40 U, GeneWorks, Adelaide, South Australia, Australia), 3 lL 10 mM dNTPs, 15 lL 2nd strand buffer [200 mM Tris pH 6.9, 46 mM MgCl2, 900 mM KCl, 100 mM (NH4)2SO4, 1.5 mM NAD] and 105 lL H2O were added. After incubation at 16 C for 2 h, 2 lL T4 DNA polymerase (10 U, New England Biolab) were added; samples were incubated at 16 C for 15 min and heat inactivated at 70 C for 10 min. Double-stranded cDNA was extracted with 150 lL phenol : chloroform (1 : 1) and washed three times with 500 lL Rnase-free H2O in a Microcon YM-30 (Millipore, Sydney, New South Wales, Australia) filter. The cDNA was recovered and the volume adjusted to 8 lL. To the concentrated cDNA, 2 lL each of ATP, GTP, CTP, UTP (75 mM), 10· transcription buffer and MEGAscript T7 enzyme mix (Ambion, Adelaide, South Australia, Australia) were added and the solution incubated at 37 C for 4–16 h to allow in vitro transcription. The aRNA was extracted with TRIzol according to the manufacturer’s instructions.

treatment_protocol: Cases were classified into alcoholics (A: ≥80 g of ethanol per day or diagnosed as long-term alcoholic), non alcoholics (NA: ≤30 g of ethanol per day, no history of alcohol abuse), smokers (S: ≥5 cigarettes per day or diagnosed as heavy smoker) and non smokers (NS: never smoked).

tag: sample

value: smoking alcoholic_array 13422306

tag: sex

value: male

tag: cause of death

value: bleeding oesophageal varices

source_name: nucleus accumbens, reference pool

value: pool of individual samples


title: smoking alcoholic3

value: smoking alcoholic_array 13433290

value: ischemic heart disease, emphysema


title: smoking alcoholic5

value: smoking alcoholic_array 13433288

value: respiratory failure, pneumonia


title: smoking alcoholic4

value: smoking alcoholic_array 13427608

value: suicide by hanging


title: B6-Lystbg-J, biological rep1

description: B6-Lystbg-J, biological rep1

source_name: 60 day old B6-Lyst iris


title: C57BL/6J iris, biological rep3

description: C57BL/6J iris, biological rep3

source_name: 60 day old C57BL/6J iris


title: B6-Lystbg-J, biological rep2

description: B6-Lystbg-J, biological rep2


title: smoking alcoholic2

value: smoking alcoholic_array 13422330

value: alcohol intoxication


title: C57BL/6J iris, biological rep2

description: C57BL/6J iris, biological rep2


title: B6-Lystbg-J, biological rep3

description: B6-Lystbg-J, biological rep3


title: Indica*Japonica 1

city: New Haven

first: Hang

last: He

state: CT

address: 165 Prospect St

department: MCDB

institute: Yale University

hyb_protocol: Sample Hybridization protocol provided and performed by NimbleGen.

scan_protocol: Nimblegen. Sample scan protocol provided and performed by NimbleGen.

data_processing: refer to NMPP, A user-customized NimbleGen Microarray Processing Pipeline, By Xiangfeng Wang

organism: Oryza sativa

source_name: shoot tissue from seedling in Indica*Japonica

label_protocol: The aa-dUTP decorated cDNA was fluorescent labeled by conjugating the monofunctional Cy3 dye (GE Healthcare, Piscataway, NJ) to the amino-allyl functional groups in the cDNA. Two μg dye-labeled targets were used for hybridization.

growth_protocol: The shoot tissue from seedling grown in environmentally controlled growth chambers at 34 °C were harvested at the four-leaf stage

extract_protocol: Total RNA and mRNA were sequentially isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen) according to the manufacturer’s recommendations, respectively. mRNA from different organ types was reverse transcribed using a mixture of oligo(dT)18 and random nonamer primers, during which amino-allyl-modified dUTP (aa-dUTP) was incoporated.

treatment_protocol: Frozen in liquid nitrogen and homogenized. Total RNA and polyA (+) RNA were subsequently isolated using the RNeasy Plant Mini kit (Qiagen) and the Oligotex mRNA kit (Qiagen) according to the manufacturer’s recommendations, respectively.

value: shoot


title: non smoking alcoholic4

source_name: nucleus accumbens, alcoholic non smoker

value: non smoking alcoholic_array 13438004

value: cardiomyopathy


title: Japonica*Indica 1

source_name: shoot tissue from seedling in Japonica*Indica

growth_protocol: The shoot tissue from seedling grown in environmentally controlled growth chambers at 37 °C were harvested at the four-leaf stage


title: non smoking alcoholic3

value: non smoking alcoholic_array 13465600

value: female

value: mixed drug toxicity, chronic alcoholism


title: C57BL/6J iris, biological rep1

description: C57BL/6J iris, biological rep1

value: 60 day old

value: adult iris


title: Indica:Japonica = 2:2

source_name: shoot tissue from seedling, titration with Indica:Japonica = 2:2

growth_protocol: The shoot tissue from seedling grown in environmentally controlled growth chambers at 32 °C were harvested at the four-leaf stage


title: Indica*Japonica 2

growth_protocol: The shoot tissue from seedling grown in environmentally controlled growth chambers at 35 °C were harvested at the four-leaf stage


title: non smoking alcoholic2

value: non smoking alcoholic_array 13438007

value: male

value: sepsis

value: pool of individual samples


title: Indica:Japonica = 1:2

source_name: shoot tissue from seedling, titration with Indica:Japonica = 1:2

growth_protocol: The shoot tissue from seedling grown in environmentally controlled growth chambers at 30 °C were harvested at the four-leaf stage


title: Indica*Japonica 3

growth_protocol: The shoot tissue from seedling grown in environmentally controlled growth chambers at 36 °C were harvested at the four-leaf stage


title: Japonica*Indica 2

growth_protocol: The shoot tissue from seedling grown in environmentally controlled growth chambers at 38 °C were harvested at the four-leaf stage


title: Japonica*Indica 3

growth_protocol: The shoot tissue from seedling grown in environmentally controlled growth chambers at 39 °C were harvested at the four-leaf stage


title: Indica:Japonica = 1:1

source_name: shoot tissue from seedling, titration with Indica:Japonica = 1:1

growth_protocol: The shoot tissue from seedling grown in environmentally controlled growth chambers at 31 °C were harvested at the four-leaf stage


title: non smoking alcoholic5

value: non smoking alcoholic_array 13422331

value: acute alcohol poisoning


title: smoking non alcoholic4

source_name: nucleus accumbens, non alcoholic smoker

value: smoking non alcoholic_array 13422318

value: atherosclerotic cardiovascular disease


title: smoking non alcoholic3

value: smoking non alcoholic_array 13465604

value: ischemic heart disease


title: non smoking non alcoholic5

source_name: nucleus accumbens, non alcoholic non smoker

value: non smoking non alcoholic_array 13427615


title: smoking non alcoholic1

value: smoking non alcoholic_array 13427607

value: coronary artery atheroma


title: non smoking non alcoholic4

value: non smoking non alcoholic_array 13427605


title: smoking non alcoholic5

value: smoking non alcoholic_array 13422301

value: atherosclerotic coronary heart disease


title: non smoking non alcoholic3

value: non smoking non alcoholic_array 13427609

value: female


title: non smoking alcoholic1

value: non smoking alcoholic_array 13422319

value: male

value: consequences of cirrhosis


title: non smoking non alcoholic2

value: non smoking non alcoholic_array 13422304

value: dilated cardiomyopathy

value: pool of individual samples


title: Indica:Japonica = 1:4

source_name: shoot tissue from seedling, titration with Indica:Japonica = 1:4

growth_protocol: The shoot tissue from seedling grown in environmentally controlled growth chambers at 29 °C were harvested at the four-leaf stage

value: shoot


title: Indica:Japonica = 4:2

source_name: shoot tissue from seedling, titration with Indica:Japonica = 4:2

growth_protocol: The shoot tissue from seedling grown in environmentally controlled growth chambers at 33 °C were harvested at the four-leaf stage


title: Indica:Japonica = 0:2

source_name: shoot tissue from seedling, titration with Indica:Japonica = 0:2

growth_protocol: The shoot tissue from seedling grown in environmentally controlled growth chambers at 28 °C were harvested at the four-leaf stage


title: non smoking non alcoholic1

value: non smoking non alcoholic_array 13438118

value: respiratory arrest


title: smoking non alcoholic2

value: smoking non alcoholic_array 13427606

value: coronary thrombosis


title: endometrium, day 8, non-pregnant, mare#6

status: Public on Jun 30 2010

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

description: endometrial tissue sample collected from day 08 non-pregnant mare

hyb_protocol: Microarray analysis was performed using Agilent 4x44k Horse Gene Expression microarrays (AMADID 021322). Labeled cRNA was hybridized to the microarrays according the manufacturer’s instructions.

scan_protocol: Hybridized and washed slides were scanned at 3 µm resolution with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies).

data_processing: Image processing was performed with Feature Extraction Software 10.5.1.1 (Agilent Technologies). Processed signals were filtered based on “Well above background” flags (detection in 4 of 6 samples in either one of the two experimental groups) and subsequently normalized with the BioConductor package vsn.

organism: Equus caballus

source_name: endometrium, day 08, non-pregnant

label_protocol: Cy3-labeled cRNA was produced using the Quick Amp Labeling Kit, one-color (Agilent Technologies) according the manufacturer’s instructions.

extract_protocol: Total RNA was isolated from the 12 endometrial biopsy samples using Trizol® Reagent (Invitrogen GmbH, Karlsruhe, Germany) according to the manufacturer’s instructions. Quantity and purity of RNA were measured with a NanoDrop 1000 (PEQLAB Biotechnologie GMBH, Erlangen, Germany). Quality of total RNA was determined by electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). RNA integrity (RIN) values ranged from 8.3 to 9.2.

tag: breed

value: warmblood

tag: mare#

tag: pregnancy

value: control

value: endometrial tissue

tag: time

value: 8 d


title: endometrium, day 8, non-pregnant, mare#2


title: endometrium, day 8, pregnant, mare#2

description: endometrial tissue sample collected from day 08 pregnant mare after embryo recovery

source_name: endometrium, day 08, pregnant

value: pregnant


title: endometrium, day 8, pregnant, mare#6


title: endometrium, day 8, pregnant, mare#5


title: endometrium, day 12, pregnant, mare#3

description: endometrial tissue sample collected from day 12 pregnant mare after embryo recovery

source_name: endometrium, day 12, pregnant


title: endometrium, day 12, non-pregnant, mare#6

description: endometrial tissue sample collected from day 12 non-pregnant mare

source_name: endometrium, day 12, non-pregnant


title: endometrium, day 8, non-pregnant, mare#5


title: endometrium, day 8, pregnant, mare#1


title: endometrium, day 8, non-pregnant, mare#1


title: endometrium, day 12, pregnant, mare#5


title: endometrium, day 12, non-pregnant, mare#5


title: endometrium, day 12, pregnant, mare#6


title: endometrium, day 8, pregnant, mare#4


title: endometrium, day 12, non-pregnant, mare#1


title: endometrium, day 12, non-pregnant, mare#4


title: endometrium, day 12, pregnant, mare#4


title: endometrium, day 8, non-pregnant, mare#4


title: endometrium, day 12, pregnant, mare#2


title: endometrium, day 12, non-pregnant, mare#2


title: endometrium, day 12, non-pregnant, mare#3


title: endometrium, day 12, pregnant, mare#1


title: 166-NA-7d-R2 vs 166-A-2d-R2

city: Lubbock

first: Kameswara Rao

last: Kottapalli

state: TX

address: 3810 4th Street

department: Plant & Soil Science

institute: USDA-ARS Lubbock & Texas Tech University

description:
Keyword = peanut
Keyword = Heat stress

hyb_protocol: Standard protocol of Gene Expression Hybridization Kit from Agilent Technologies.

scan_protocol: Standard protocol of GenePix 4000B Microarray Scanner

data_processing: Feature Extraction software Version 9.5 from Agilent Technologies

organism: Arachis hypogaea

source_name: Susceptible Non Acclimated 7day _Replication2

label_protocol: Standard Protocol of Agilent Low RNA Input Fluorescent Linear Amplification Kit.

growth_protocol: Plants were raised in the greenhouse and tissue samples were harvested on 52 DAS.

extract_protocol: Total RNA was extracted using Qiagen Rneasy Plant Maxi Kit according to manufacturer's protocol.

treatment_protocol: Plants directly exposed to a maximum temperature of 45C at 12.00 Noon on 45th day. Samples collected 7 days after stress.

value: leaf

tag: genotype

source_name: Susceptible Acclimated 2day _Replication2

growth_protocol: Plants were raised in the walking chambers and tissue samples were harvested on 47 DAS.

treatment_protocol: Plants acclimated to 45C for 1 day and then recovered from stress by growing them at ambient temperature for 7 days. Acclimated plants exposed to a maximum temperature of 45C at 12.00 Noon on 45th day. Samples collected on 2nd day after stress.


title: 041-NA-0d-R2 vs 041-A-2d-R2

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant Non Acclimated 0day _Replication2

growth_protocol: Plants were raised in the greenhouse and tissue samples were harvested on 45 DAS.

treatment_protocol: No treatment

source_name: Tolerant Acclimated 2day _Replication2


title: 166-A-7d-R2 vs 041-NA-3dPR-R2

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible Acclimated 7day _Replication2

growth_protocol: Plants were raised in the walking chambers and tissue samples were harvested on 52 DAS.

treatment_protocol: Plants acclimated to 45C for 1 day and then recovered from stress by growing them at ambient temperature for 7 days. Acclimated plants exposed to a maximum temperature of 45C at 12.00 Noon on 45th day. Samples collected on 7th day after stress.

source_name: Tolerant Non Acclimated 3day post recovery_Replication2

growth_protocol: Plants were raised in the greenhouse and tissue samples were harvested on 62 DAS.

treatment_protocol: Plants directly exposed to a maximum temperature of 45C at 12.00 Noon on 45th day. After 14 days stress plants were brought to ambient temperature and recovered from stress for 3 days.


title: 041-A-0d-R2 vs 041-A-3dPR-R2

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant Acclimated 0day _Replication2

growth_protocol: Plants were raised in the walking chambers and tissue samples were harvested on 45 DAS.

treatment_protocol: Plants acclimated to 45C for 1 day and then recovered from stress by growing them at ambient temperature for 7 days. Samples collected just before starting stress.

source_name: Tolerant Acclimated 3day post recovery_Replication2

growth_protocol: Plants were raised in the walking chambers and tissue samples were harvested on 62 DAS.

treatment_protocol: Plants acclimated to 45C for 1 day and then exposed to a maximum temperature of 45C at 12.00 Noon. After 14 days stress plants were brought to ambient temperature and recovered from stress for 3 days.


title: 166-NA-2d-R2 vs 166-NA-0d-R2

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible Non Acclimated 2day _Replication2

growth_protocol: Plants were raised in the greenhouse and tissue samples were harvested on 47 DAS.

treatment_protocol: Plants directly exposed to a maximum temperature of 45C at 12.00 Noon on 45th day. Samples collected 2 days after stress.

source_name: Susceptible Non Acclimated 0day _Replication2

treatment_protocol: No Treatment


title: 041-A-7d-R2 vs 166-A-7d-R1

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant Acclimated 7day _Replication2

source_name: Succeptible Acclimated 7day _Replication1


title: 166-NA-3dPR-R1 vs 166-NA-2d-R1

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible Non Acclimated 3day post recovery_Replication1

source_name: Susceptible Non Acclimated 2day_Replication1

treatment_protocol: Plants directly exposed to a maximum temperature of 45C at 12.00 Noon on 45th day.


title: 166-A-0d-R2 vs 041-A-0d-R1

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible Acclimated 0day _Replication2

source_name: Tolerant Acclimated 0day _Replication1


title: 041-NA-3dPR-R1 vs 041-NA-2d-R2

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant Non Acclimated 3day post recovery_Replication1

source_name: Tolerant Non Acclimated 2day _Replication2


title: 041-A-3dPR-R1 vs 041-A-7d-R1

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant Acclimated 3day post recovery_Replication1

treatment_protocol: Plants acclimated to 45C for 1 day and then exposed to a maximum temperature of 45C at 12.00 Noon on 45th day. After 14 days stress plants were brought to ambient temperature and recovered from stress for 3 days.

source_name: Tolerant Acclimated 7day_Replication1


title: 041-NA-2d-R1 vs 041-NA-0d-R1

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant Non Acclimated 2day _Replication1

source_name: Tolerant Non Acclimated 0day _Replication1


title: 041-NA-7d-R2 vs 166-NA-3dPR-R2

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant Non Acclimated 7day _Replication2

treatment_protocol: Plants directly exposed to a maximum temperature of 45C at 12.00 Noon. Samples collecte 7 days after stress.

source_name: Susceptible Non Acclimated 3day post recovery_Replication2


title: 166-A-2d-R1 vs 166-A-3dPR-R2

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible Acclimated 2day _Replication1

treatment_protocol: Plants acclimated to 45C for 1 day and then exposed to a maximum temperature of 45C at 12.00 Noon on 45th day.

source_name: Susceptible Acclimated 3day post recovery_Replication2


title: R3-T-12h vs R3-S-48h HSMA-03_4

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant 12h_Replication3

label_protocol: Standard Protocol of Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were raised in the greenhouse and tissue samples were harvested from convirons on 45 DAS.

extract_protocol: Total RNA was extracted using Qiagen Rneasy Plant Maxi Kit according to manufacturer’s protocol.

treatment_protocol: Plants exposed to a maximum temperature of 45C at 12.00 Noon

tag: stress condition

value: heat

tag: stress time

source_name: Susceptible 48h _Replication3

growth_protocol: Plants were raised in the greenhouse and tissue samples were harvested from convirons on 47 DAS.


title: R2-T-0h vs R2-T-24h HSMA-02_4

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant 0h_Replication2

extract_protocol: Total RNA was extracted using Qiagen Rneasy Plant Maxi Kit according to manufacturers protocol.

source_name: Tolerant 24h_Replication2

growth_protocol: Plants were raised in the greenhouse and tissue samples were harvested from convirons on 46 DAS.


title: R3-T-24h vs R3-S-12h HSMA-03_3

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant 24h_Replication3

source_name: Susceptible 12h _Replication3


title: R2-T-48h vs R1-T-12h HSMA-02_2

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant 48h_Replication2

source_name: Tolerant 12h_Replication1


title: R2-S-0h vs R2-S-24h HSMA-01_4

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible 0h _Replication2

source_name: Susceptible 24h _Replication2


title: R3-T-0h vs R3-T-48h HSMA-03_2

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant 0h_Replication3

source_name: Tolerant 48h_Replication3


title: R1-S-12h vs R1-S-0h HSMA-01_2

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible 12h _Replication1

source_name: Susceptible 0h _Replication1


title: R3-S-24h vs R1-T-24h HSMA-02_3

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible 24h _Replication3

growth_protocol: Plants were raised in the greenhouse and tissue samples were harvested on 46 DAS.

source_name: Tolerant 24h_Replication1


title: 041-A-2d-R1 vs 041-NA-7d-R1

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant Acclimated 2day _Replication1

source_name: Tolerant Non Acclimated 7day _Replication1


title: 166-NA-0d-R1 vs 166-NA-7d-R1

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible Non Acclimated 0day _Replication1

source_name: Susceptible Non Acclimated 7day _Replication1


title: R2-S-12h vs R2-S-48h HSMA-02_1

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible 12h _Replication2

source_name: Susceptible 48h _Replication2


title: 4823936053_J

status: Public on Jun 16 2010

city: Augusta

first: yewei

last: xing

state: GA

address: 1120 15th street

department: Physiology

institute: Medical College of Georgia

description: triplicate 2 (ACTH)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data is generated through GenomeStudio software.  The raw data were normalised using quantile normalisation with IlluminaGUI in R. Genespring 11 software was used for subsequent data analysis.

source_name: human primary adult adrenal cells

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

extract_protocol: RNA was extracted with  QIAGEN Rneasy plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: agent

value: ACTH


title: 2 Gy irradiated hESCs, Replicate 3

city: Stanford

first: Kitchener

middle: D.

last: Wilson

address: S140 Grant Bldg

hyb_protocol: 825 ng of Cy3- and Cy5- labeled and amplified cRNA was mixed and fragmented according to the Agilent technology protocol. cRNA was hybridized to 4x44K whole human genome microarray slides from Agilent (Part G4112F) according to the manufacturer’s instructions. The hybridization was carried in a rotating hybridization chamber in the dark at 65°C for 17 h.

scan_protocol: The arrays were scanned using Agilent G2505B DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.5.1 applying LOWESS background subtraction and dye-normalization. For probe selection criteria, 6 of 12 microarrays were required to have flags that were present or marginal.  One sample (0.4Gy-3) was excluded from  the analysis because it appeared to be an outlier compared to the other samples.

source_name: irradiated H9 hESCs

label_protocol: Using Low RNA Input Fluorescent Linear Amplification Kits (Agilent), cDNA was reverse transcribed from each RNA sample, as well as from a pooled reference control, and cRNA then transcribed and fluorescently labeled with Cy5/Cy3. cRNA was purified using an RNeasy kit (Qiagen).

growth_protocol: hESCs were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes with mTESR-1 human ES Growth Medium (StemCell Technologies).

extract_protocol: Total RNA was prepared using RNeasy Mini Kit (Qiagen)

value: H9 embryonic stem cells (hESCs)

tag: differentiation state

value: undifferentiated

tag: treatment group

value: 2 Gy irradiated

source_name: Pooled RNA reference

value: pool of undifferentiated and differentiated hESCs, as well as fetal and neonatal tissues


title: 4823936053_L

description: triplicate 2 (ACTH)


title: 4823936053_G

description: triplicate 1 (Basal)


title: 2 Gy irradiated hESCs, Replicate 2

tag: cell type


title: 4823936053_H

description: triplicate 2 (ACTH)


title: 4 Gy irradiated hESCs, Replicate 2

value: 4 Gy irradiated


title: 120208_Rainey_48h_Basal#2_Sample_Probe_Profile

description: triplicate 1(Basal)

data_processing: The raw data is generated through GenomeStudio software. The raw data were normalised using quantile normalisation with IlluminaGUI in R. Genespring 11 software was used for subsequent data analysis.

source_name: human primary fetal adrenal cells


title: 4 Gy irradiated hESCs, Replicate 1


title: 4823936053_K

description: triplicate 1 (Basal)


title: R1-S-48h vs R1-T-0h

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible 48h _Replication1

source_name: Tolerant 0h_Replication1

extract_protocol: Total RNA was extracted using Qiagen Rneasy Plant Maxi Kit according to manufacturers protocol


title: 4 Gy irradiated hESCs, Replicate 3


title: R2-T-12h vs R3-S-0h HSMA-03_1

description:
Keyword = peanut
Keyword = Heat stress

source_name: Tolerant 12h_Replication2

source_name: Susceptible 0h _Replication3


title: 120208_Rainey_48h_ACTH#2_Sample_Probe_Profile

description: triplicate 2 (ACTH)


title: 4823936053_I

description: triplicate 1 (Basal)


title: 042409_Rainey_Yewei_HFA-48h-ACTH_Sample_Probe_Profile

description: triplicate 2 (ACTH)


title: 120208_Rainey_48h_ACTH#1_Sample_Probe_Profile

description: triplicate 2 (ACTH)


title: R1-S-24h vs R1-T-48h HSMA-01_3

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible 24h _Replication1

source_name: Tolerant 48h_Replication1


title: 120208_Rainey_48h_Basal#1_Sample_Probe_Profile

description: triplicate 1(Basal)


title: 2 Gy irradiated hESCs, Replicate 1


title: Rhodospirillum rubrum S1H in RWV liquid Sistrom DAE

status: Public on Jun 05 2010

city: MOL

first: Natalie

last: Leys

state: Please select one below:

address: 200, boeretang

department: Institute for Environment, Health & Safety

country: Belgium

description: no additional information

hyb_protocol: The two differentially labeled cDNAs were resuspended in the universal hybridization buffer (Pronto kit; Corning-Promega, United States), mixed, and added jointly to the surface of the spotted microarray glass slide for overnight hybridization at 42°C using a HS 4800 Pro automated hybridization station (TECAN, Switzerland). The slide was washed according to the Pronto kit’s protocol and then dried in the hybridization station.

data_processing: Spots were analyzed using GenePix Pro v.6.0.1 software and flagged according to their quality. Quality check was performed for each array using the ArrayQuality package from BioConductor (Gentleman et al, 2004). Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.14.1 (Smyth, 2005) as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50 (Ritchie et al, 2007). Data were normalized within each array using the loess normalization algorithm (Smyth and Speed, 2003) and between each array using Aquantile normalization (Yang and Thorne, 2003). The in-slide replicate correlations were calculated using the Duplicate correlation function in the LIMMA package (Smyth et al, 2005). The log expression values were fit to a linear model and moderated t-statistics were calculated using empirical Bayes method (Smyth, 2004). P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate (Benjamini and Hochberg, 1995).

organism: Rhodospirillum rubrum

source_name: Rhodospirillum rubrum S1H RWV control Sistrom liquid

label_protocol: Ten micrograms of RNA was reverse transcribed by random priming according to the Pronto kit’s instructions (Corning-Promega, United States) and directly labeled by incorporation of Cy3-dCTP or Cy5-dCTP nucleotides (Amersham Bioscience, United Kingdom) for respectively control and experimental samples.

extract_protocol: Total RNA was extracted using a SV Total RNA Isolation System kit (Promega, United States) and stored at -80 °C. The quality/integrity of total RNA was checked using a BioAnalyzer 2100 (Agilent, United States) and total RNA quantity was measured using the NanoDrop ND-1000 spectrophotometer (NanoDrop technologies, United States).

treatment_protocol:
All cultures were allowed to grow for 10 days at 21 °C which are typical time frame and growth temperature of a Soyuz space flight mission (Mastroleo et al., 2009). The RWV (rotating wall vessels) bioreactors (Cellon, Bereldange, Luxembourg) were filled completely with ca. 58 ml of culture medium containing 1 % inoculum from the stock culture. Air bubbles were carefully removed through the sampling ports, using syringes (without needle), in order to avoid undesired shear stress. The vessels were mounted on a RWV device placed in horizontal position.
Gas exchange in the RWV bioreactors during growth was ensured by the gas-permeable silicone membrane present at the back of each RWV culture vessel. Bacterial growth in RWV conditions was allowed at a rotational speed of 25 rpm. After cultivation, oxygen concentration was measured by inserting the oxygen probe directly into the vessel without homogenization. After homogenization, optical density was measured at 600 nm and cells were harvested for pigment quantification as previously described (Favier-Teodorescu, 2004) and for transcriptomic and proteomic analysis.

tag: sample type

value: Three independent cultures of R. rubrum S1H grown to stationary phase in Sistrom-succinate medium A containing 2 g/L Na-succinate (Sistrom, 1960) in dark aerobic conditions were resuspended in 0.85 % NaCl  to a final OD680 of ca. 0.600 to constitute stock cultures

source_name: Rhodospirillum rubrum S1H RWV Sistrom liquid

treatment_protocol:
All cultures were allowed to grow for 10 days at 21 °C which are typical time frame and growth temperature of a Soyuz space flight mission (Mastroleo et al., 2009). The RWV bioreactors (Cellon, Bereldange, Luxembourg) were filled completely with ca. 58 ml of culture medium containing 1 % inoculum from the stock culture. Air bubbles were carefully removed through the sampling ports, using syringes (without needle), in order to avoid undesired shear stress. The vessels were mounted on a RWV device and were placed in a culture chamber, in vertical position creating the low-shear modeled microgravity (LSMMG) environment
Gas exchange in the RWV bioreactors during growth was ensured by the gas-permeable silicone membrane present at the back of each RWV culture vessel. Bacterial growth in RWV conditions was allowed at a rotational speed of 25 rpm. After cultivation, oxygen concentration was measured by inserting the oxygen probe (ref. type to be added) directly into the vessel without homogenization. After homogenization, optical density was measured at 600 nm and cells were harvested for pigment quantification as previously described (Favier-Teodorescu, 2004) and for transcriptomic and proteomic analysis.


title: 0.4 Gy irradiated hESCs, Replicate 3

value: 0.4 Gy irradiated


title: Rhodospirillum rubrum S1H in RPM liquid Sistrom DAE

description: no additional information

scan_protocol: The two differentially labeled cDNAs were resuspended in the universal hybridization buffer (Pronto kit; Corning-Promega, United States), mixed, and added jointly to the surface of the spotted microarray glass slide for overnight hybridization at 42°C using a HS 4800 Pro automated hybridization station (TECAN, Switzerland). The slide was washed according to the Pronto kit’s protocol and then dried in the hybridization station.

source_name: Rhodospirillum rubrum S1H RPM control Sistrom liquid

treatment_protocol:
All cultures were allowed to grow for 10 days at 21 °C which are typical time frame and growth temperature of a Soyuz space flight mission (Mastroleo et al., 2009). The RWV (rotating wall vessels) bioreactors (Cellon, Bereldange, Luxembourg) were filled completely with ca. 58 ml of culture medium containing 1 % inoculum from the stock culture. Air bubbles were carefully removed through the sampling ports, using syringes (without needle), in order to avoid undesired shear stress. The vessels were mounted on RWV vessel device placed in horizontal position.
Gas exchange in the RWV bioreactors during growth was ensured by the gas-permeable silicone membrane present at the back of each RWV culture vessel. Bacterial growth in RWV conditions was allowed at a rotational speed of 25 rpm. After cultivation, oxygen concentration was measured by inserting the oxygen probe directly into the vessel without homogenization. After homogenization, optical density was measured at 600 nm and cells were harvested for pigment quantification as previously described (Favier-Teodorescu, 2004) and for transcriptomic and proteomic analysis.

tag: strain

value: Four independent cultures of R. rubrum S1H grown to stationary phase in Sistrom-succinate medium A containing 2 g/L Na-succinate (Sistrom, 1960) in dark aerobic conditions were resuspended in 0.85 % NaCl  to a final OD680 of ca. 0.600 to constitute stock cultures.

source_name: Rhodospirillum rubrum S1H RPM Sistrom liquid

treatment_protocol:
All cultures were allowed to grow for 10 days at 21 °C which are typical time frame and growth temperature of a Soyuz space flight mission (Mastroleo et al., 2009). The RWV bioreactors (Cellon, Bereldange, Luxembourg) were filled completely with ca. 58 ml of culture medium containing 1 % inoculum from the stock culture. Air bubbles were carefully removed through the sampling ports, using syringes (without needle), in order to avoid undesired shear stress. The vessels were mounted on a RPM device operated as a random walk three-dimensional clinostat (basic mode) with an angular velocity of rotation of 60 deg s-1 as previously described (Mastroleo et al., 2009).
Gas exchange in the RWV bioreactors during growth was ensured by the gas-permeable silicone membrane present at the back of each RWV culture vessel. Bacterial growth in RWV conditions was allowed at a rotational speed of 25 rpm. After cultivation, oxygen concentration was measured by inserting the oxygen probe (ref. type to be added) directly into the vessel without homogenization. After homogenization, optical density was measured at 600 nm and cells were harvested for pigment quantification as previously described (Favier-Teodorescu, 2004) and for transcriptomic and proteomic analysis.


title: Control (non-irradiated) hESCs, Replicate 1

source_name: non-irradiated H9 hESCs

value: non-irradiated


title: Control (non-irradiated) hESCs, Replicate 3


title: 0.4 Gy irradiated hESCs, Replicate 2


title: 0.4 Gy irradiated hESCs, Replicate 1


title: V campbellii, biological rep5

status: Public on Jun 01 2010

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

description: Gene expression data from V. campbellii at Mid-log phase

hyb_protocol: The cocktail was prepared according to Affymetrix standard protocol, and hybridized onto the Custom design Vharveyi520694 arrays (affymetrix). Hybridization was carried out for 16 h at 49 °C with rotation at 60 rpm. The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip 7G Scanner.

scan_protocol: The microarrays were scanned using the GeneChip 7G Scanner (Affymetrix.   GeneChip® Operating Software 1.4 (GCOS 1.4) (Affymetrix) was used to acquire and process array images Microarray Suite 5.0 (MAS5) algorithm, and generated the Report files summarizing

data_processing: CEL files were processed using the GeneChip® Operating Software 1.4 (GCOS 1.4) (Affymetrix) to get signal intensity.

label: Biotin

organism: Vibrio campbellii CAIM 519 = NBRC 15631 = ATCC 25920

source_name: ATCC-BAA1116 V. campbellii at mid-log phase

label_protocol: Target Preparation and Hybridization to Arrays: 1 µg of mRNA contained PolyA RNA controls (Affymetrix, Santa Clara, CA) with known concentrations to monitor the quality of the procedures .  The labeling reaction is carried out in 30 uL reaction volume using KREATECH’s aRNA Labeling Kit (KREATECH Biotechnology, Amsterdam, the Netherlands) according to the manufacture’s recommended protocol.  Labeled mRNAs were purified and fragmented using fragmentation buffer from Ambion (Austin, TX).  Fragmentation  reaction was carried out in a reaction volume of 33 uL  using fragmentation buffer from Ambion.

growth_protocol: V. campbellii were grown in 50 mL polypropylene centrifuge tubes containing 5 mL of Luria Marine media and were incubated at 30°C for 12 hours with 250 rpm agitation until it reach cell density at Mid-log phase, 1.0E+8 to 1.0E+10 cells.  Diploid strains MLY61 a/alpha (ura3-52/ura3-52 MATa/alpha) and MLY132 a/alpha (delta gpa2::G418/delta gpa2::G418 ura3-52/ura3-52 MATa/alpha) were obtained from J. Heitman, Duke University{Lorenz, 2000 #19; Lorenz, 1997 #33}. Standard YPM media were used as described{Sherman, 1991 #36}. Synthetic low ammonium media consisting of SLAM (0.17% Yeast Nitrogen Base without ammonium sulfate or amino acids, 50 µM ammonium sulfate, 2% maltose) were used when switching to low nitrogen pseudohyphal inducing conditions{Lorenz, 2000 #19; Lorenz, 1997 #33}. Similar to a previously described method{Pan, 2000 #37}, strains were grown to an OD600 of 1.0 in YPM media. Approximately 200 OD600 units were collected by filtering followed by resuspension in 10 mL RNAlater (Ambion) for <30 min, pelleted by centrifugation, flash frozen and stored at –80 °C. Strains were also grown to an OD600 of 1.0 in YPM media and approximately 200 O.D. were collected by filtration and transferred to SLAM media for 2 h at 30 °C prior to collection as above.

extract_protocol: Total RNA were extracted using RiboPure Bacteria Kit (Ambion Inc., Austin, TX) according to the manufacturer's instructions with adjustment of the volume of ethanol (1.25 instead of 0.5) added to the aqueous phase to capture small RNA. mRNA enrichment were performed with 10 ug total RNA using using the MICROBExpress kit (Ambion) according to the manufacturer’s protocol. The quantity of mRNA samples were determined by NanoDrop ND1000 (Thermo Scientific Inc., Waltham, MA) spectrophotometer.

tag: growth phase

value: Mid-log phase


title: 042409_Rainey_Yewei_HFA-48h-Basal_Sample_Probe_Profile

description: triplicate 1(Basal)

value: control


title: V campbellii, biological rep2


title: V campbellii, biological rep1


title: V campbellii, biological rep3


title: V campbellii, biological rep4


title: Control (non-irradiated) hESCs, Replicate 2


title: IR2

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description: Replicate 2

data_processing: Data was normalized in BeadStudio 2.0 using Cubic Spline normalization method. The data was exported and then imported into Genespring 7.3 where it was filtered on expression levels and p-value detection. Volcano plot between the 2 groups using fold change and p-values was used to find the significant genelist.

organism: Rattus norvegicus

source_name: IR Retina

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

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

value: Sprague-Dawley

tag: tissue

value: retina

value: transient ischemia followed by reperfusion (IR)


title: IR5

description: Replicate 5


title: IR3

description: Replicate 3


title: Control4

description: Replicate 4

source_name: Control Retina


title: Control5

description: Replicate 5


title: Control6

description: Replicate 6


title: IR4

description: Replicate 4


title: IR1

description: Replicate 1


title: Control2

description: Replicate 2


title: IR6

description: Replicate 6


title: Control3

description: Replicate 3


title: Control1

description: Replicate 1


title: RNA from Nurr1-infected neurons

city: Stockholm

first: Nikolaos

last: Volakakis

address: Nobels vag 3

country: Sweden

institute: LICR

description: Affymetrix Genechip scanner 3000 7G

hyb_protocol: After hybridization, the arrays were washed and stained in fluidics station FS-450 according to the standard Affymetrix protocol.

scan_protocol: Affymetrix Genechip scanner 3000 7G

data_processing: Affymetrix GeneChip Operating software version 1.4. To allow comparisons of transcript levels, all samples were subjected to an all-probe set scaling to target signal 100.

source_name: Nurr1-infected neurons

label_protocol: Affymetrix 3' IVT express kit

extract_protocol: Qiagen mini kit

value: ES-cell derived neurons

tag: genome/variation


title: Epi_200_16h_0.1Gy, 2

city: New York

first: Alexandre

last: Mezentsev

state: NY

address: 630 west 168th Street, VC 15-204

department: Dermatology

institute: Columbia University

description: Gene expression in 0.1 Gy-proton irradiated tissue model, 16h postirradiation

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v1_91_1 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not 'Well above background' were excluded

source_name: human foreskin

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Samples were supplied on ice with overnight delivery and were cultured 24 h prior irradiation and indicated time prior harvesting, postirradiation. Growth medium, NMM-100, was kindly supplied by the manufacturer. Medium was changed every 24h.

extract_protocol: Total RNA was isolated with RNaqueous Kit (Applied Biosystems), tested for spectral characteristics (NanoDrop, Thermo Scientific) and electrophoretically (Bioanalyser 2100, Agilent).

treatment_protocol: Tissues were irradiated with 0, 0.1 and 2.5Gy of protons

value: epidermis

tag: gender

value: male

tag: time point

tag: dose


title: Epi_200_16h_2.5Gy, 2

description: Gene expression in 2.5 Gy-proton irradiated tissue model, 16h postirradiation


title: Epi_200_16h_0.1Gy, 1


title: Epi_200_24h_0.1Gy, 1

description: Gene expression in 0.1 Gy-proton irradiated tissue model, 24h postirradiation


title: Epi_200_24h_2.5Gy, 3

description: Gene expression in 2.5 Gy-proton irradiated tissue model, 24h postirradiation


title: Control

city: Guangzhou

first: Duanqing

last: Pei

state: Guangdong

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

country: China

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

description: Gene expression data from Control

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse430_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed with Robust Multichip Average (RMA) using ArrayAssist 5.0 software. Probe sets were filtered on Absolute Call(ABS_Call must be P in at least 1 of 3 samples).

source_name: cells tranduced with SKOM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3ug total RNA (Expression Analysis Technical Manual）   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: Tranduced OG2 MEFs were cultured with mESC medium. For the second group, Tgfb1 was added from day 3 to day 10 post infection. Media were changed everyday.

extract_protocol: Cells were trypsinized and feeder cells were eliminated. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: OG2 MEF were infected with Sox2, Klf4, Oct4 and c-Myc with the first group as control group, the second treated with Tgfb1, the third co-expressing Snail. Tgfb1 treatment (2ng/ml) lasted from day 3 to day 10 post infection. All samples were collected on day 10 for DNA microarray analysis.

tag: cell line

value: OG2 MEF

tag: protocol

value: SKOM transduction


title: Epi_200_24h_2.5Gy, 1


title: Epi_200_16h_2.5Gy, 3


title: Epi_200_24h_0Gy, 2

description: Gene expression in 0 Gy-proton irradiated tissue model, 24h postirradiation


title: Epi_200_24h_0.1Gy, 3


title: Epi_200_16h_0Gy, 3

description: Gene expression in 0 Gy-proton irradiated tissue model, 16h postirradiation


title: Epi_200_24h_2.5Gy, 2


title: RNA from GFP-infected neurons

description: Affymetrix Genechip scanner 3000 7G

source_name: ES-cell derived neurons

value: infected with GFP lentivirus


title: Epi_200_4h_2.5Gy, 1

description: Gene expression in 2.5 Gy-proton irradiated tissue model, 4h postirradiation


title: Epi_200_4h_0.1Gy, 3

description: Gene expression in 0.1 Gy-proton irradiated tissue model, 4h postirradiation


title: Epi_200_24h_0Gy, 1


title: Epi_200_16h_0Gy, 1


title: Epi_200_4h_2.5Gy, 3


title: Epi_200_16h_0.1Gy, 3


title: SKOM+Snail

description: Gene expression data from SKOM+Snail

source_name: cells tranduced with SKOM and Snail

value: SKOM and Snail transduction


title: SKOM+Tgfb1

description: Gene expression data from SKOM+Tgfb1

source_name: cells tranduced with SKOM plus treatment of Tgfb1

value: SKOM transduction plus Tgfb1 treatment


title: Epi_200_16h_0Gy, 2


title: 166-A-3dPR-R1 vs 166-A-0d-R1

description:
Keyword = peanut
Keyword = Heat stress

source_name: Susceptible Acclimated 3day post recovery _Replication1

growth_protocol: Plants were raised in the walking chambers and tissue samples were harvested on 62 DAS..

value: leaf

tag: genotype


title: Epi_200_4h_0.1Gy, 2


title: Epi_200_16h_2.5Gy, 1


title: Epi_200_4h_2.5Gy, 2


title: Epi_200_4h_0Gy, 2

description: Gene expression in 0 Gy-proton irradiated tissue model, 4h postirradiation


title: Epi_200_4h_0Gy, 3


title: shECAD 8

description: Gene expression data from shECAD 8

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip MoGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Partek software. Probe sets have been summaried to transcription ID using Partek software.

source_name: cells expressing E-cadherin shRNA

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: iPSCs were cultured on feeder in mESC medium. Media were changed everyday.

treatment_protocol: OG2 MEF were infected with Sox2, Klf4, Oct4 and c-Myc plus either Luciferase shRNA or E-cadherin shRNA and split onto feeder cells on Day 6 after infection. Colonies were picked on Day 14.

value: iPS clone induced from OG2 MEF

value: E-cad knockdown


title: shECAD 9

description: Gene expression data from shECAD 9


title: Ctrl 4

description: Gene expression data from Ctrl 4

source_name: cells expressing Luciferase shRNA


title: shECAD 4

description: Gene expression data from shECAD 4


title: Ctrl 3

description: Gene expression data from Ctrl 3


title: Epi_200_24h_0.1Gy, 2


title: Congenital Hypothyroidism (CH) Patient 3337

type: genomic

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

description: Array CGH analysis of a patient with Congenital Hypothyroidism

hyb_protocol: Hybridization was done overnight at 42?C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned using an Agilent scanner .PMT settings: 100/100

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalized by subgridd LOWESS. Aberrant ratios involving three or more neighbouring clones wereconsidered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Dec 2005)

molecule: genomic DNA

source_name: dna isolated from blood of a patient with ch (athreosis) gender: female

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: DNA was extracted from peripheral blood via QiaAmp DNA Blood Mini Kit Protocol (Qiagen)

treatment_protocol: sonicated

value: blood of a patient with ch (athreosis)

value: female

source_name: DNA isolated from blood of a pool of 5 healthy females

value: blood of a pool of 5 healthy females


title: Ctrl 2

description: Gene expression data from Ctrl 2

value: control


title: Congenital Hypothyroidism (CH) Patient 4255

source_name: dna isolated from blood of a patient with ch (hypoplasia) gender: male

value: blood of a patient with ch (hypoplasia)

source_name: DNA isolated from blood of a pool of 5 healthy males

value: blood of a pool of 5 healthy males


title: Congenital Hypothyroidism (CH) Patient 4291

source_name: dna isolated from blood of a patient with ch (athyreosis) gender: female

value: blood of a patient with ch (athyreosis)


title: Epi_200_4h_0Gy, 1

value: epidermis


title: Congenital Hypothyroidism (CH) Patient 3863

source_name: dna isolated from blood of a patient with ch (discordant twin to 1302) gender: female


title: PMN 6hr 11490 2

city: Hamilton

first: Addie

last: Whitney

state: MT

address: 903 S 4th St

department: LHBP

institute: NIH/NIAID/RML

description: SA-treated PMNs

hyb_protocol: cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix).  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix scanner.

data_processing: Affymetrix GeneChip Operating Software (GCOS v1.4, http://www.affymetrix.com) was used. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene.

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 11490, replicate _2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Human polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors.  PMNs were treated with hospital- and community-associated strains of S. aureus at a bacteria to PMN ratio of 10:1 for 1, 2, 3 or 6 hours at 37C.  Untreated PMNs serve as controls.

value: polymorphnuclear leukocytes

tag: treatment

value: treated with S. aureus strain 11490


title: Epi_200_4h_0.1Gy, 1

value: male


title: Congenital Hypothyroidism (CH) Patient 3707


title: PMN 6hr 11490 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 11490, replicate _3


title: Congenital Hypothyroidism (CH) Patient 2610


title: Congenital Hypothyroidism (CH) Patient 92


title: Congenital Hypothyroidism (CH) Patient 2864


title: Congenital Hypothyroidism (CH) Patient 4152

source_name: dna isolated from blood of a patient with ch (hypoplasia) gender: female


title: Congenital Hypothyroidism (CH) Patient 1302


title: Congenital Hypothyroidism (CH) Patient 3270


title: Epi_200_24h_0Gy, 3

source_name: human foreskin


title: Congenital Hypothyroidism (CH) Patient 3267


title: Congenital Hypothyroidism (CH) Patient 43

source_name: dna isolated from blood of a patient with ch (athyreosis) gender: male


title: Congenital Hypothyroidism (CH) Patient 3489


title: Congenital Hypothyroidism (CH) Patient 2562


title: Congenital Hypothyroidism (CH) Patient 32


title: Congenital Hypothyroidism (CH) Patient 19

source_name: dna isolated from blood of a patient with ch gender: female

value: blood of a patient with ch


title: Congenital Hypothyroidism (CH) Patient 3698

description: Array CGH analysis of a patient with Congenital Hypothyroidism.

scan_protocol: Slides were scanned using an Agilent scanner . PMT settings: 100/100

source_name: dna isolated from blood of a patient with ch.  gender: female

extract_protocol: DNA was extracted from peripheral blood by QiaAmp DNA Blood Mini Kit Protocol.

value: blood of a patient with ch.

source_name: DNA isolated from the blood of a donorpool of 5 healthy females.

value: blood of a donor pool of 5 healthy females.


title: Congenital Hypothyroidism (CH) Patient 3535


title: Congenital Hypothyroidism (CH) Patient 3553

source_name: dna isolated from blood of a patient with ch.  gender: male

source_name: DNA isolated from the blood of a donorpool of 5 healthy males.

value: blood of a donor pool of 5 healthy males.


title: Congenital Hypothyroidism (CH) Patient 4710


title: Congenital Hypothyroidism (CH) Patient 4618


title: Congenital Hypothyroidism (CH) Patient 4656


title: Congenital Hypothyroidism (CH) Patient 4252


title: Congenital Hypothyroidism (CH) Patient 2308


title: Congenital Hypothyroidism (CH) Patient 4174


title: Congenital Hypothyroidism (CH) Patient 4646


title: Congenital Hypothyroidism (CH) Patient 4343


title: Healthy Patient 5011, father of CH Patient 4626

source_name: dna isolated from blood of a healthy patient.  gender: male

value: blood of a healthy patient.

source_name: DNA isolated from the blood of a donorpool of 5 healthy males

value: blood of a donor pool of 5 healthy males


title: Healthy Patient 4796, mother of CH Patient 4619

source_name: dna isolated from blood of a healthy patient.  gender: female

source_name: DNA isolated from the blood of the healthy father of CH patient 4619


title: Congenital Hypothyroidism (CH) Patient 4624


title: Congenital Hypothyroidism (CH) Patient 2906


title: Congenital Hypothyroidism (CH) Patient 4650


title: Congenital Hypothyroidism (CH) Patient 4891


title: Congenital Hypothyroidism (CH) Patient 23

source_name: DNA isolated from blood of a pool of 5 healthy females


title: Congenital Hypothyroidism (CH) Patient 4855


title: Healthy Patient 4896, mother of CH Patient 1829

source_name: DNA isolated from the blood of the healthy father of CH patient 1829


title: Congenital Hypothyroidism (CH) Patient 3963


title: Healthy Patient 5044 mother of CH Patient 4607

source_name: DNA isolated from the blood of the healthy father of CH patient 4607


title: Congenital Hypothyroidism (CH) Patient 4856


title: Congenital Hypothyroidism (CH) Patient 3578


title: Congenital Hypothyroidism (CH) Patient 25b

source_name: dna isolated from blood of a patient with ch (athyreosis) gender: female


title: Congenital Hypothyroidism (CH) Patient 4880


title: Healthy Patient 3982, twin of CH Patient 3863

treatment_protocol: Whole genome amplification by GenomePlex (Sigma).

treatment_protocol: Whole genome amplification by GenomePlex(Sigma).


title: Congenital Hypothyroidism (CH) Patient 4649


title: Congenital Hypothyroidism (CH) Patient 4625


title: Congenital Hypothyroidism (CH) Patient 3501


title: Congenital Hypothyroidism (CH) Patient 2905


title: Healthy Patient 4791, mother of CH Patient 25B

source_name: DNA isolated from the blood of the healthy father of CH patient 25B


title: Congenital Hypothyroidism (CH) Patient 3542


title: Congenital Hypothyroidism (CH) Patient 4654


title: Congenital Hypothyroidism (CH) Patient 4707


title: Congenital Hypothyroidism (CH) Patient 3579


title: Congenital Hypothyroidism (CH) Patient 2788


title: Congenital Hypothyroidism (CH) Patient 2027


title: Congenital Hypothyroidism (CH) Patient 4694


title: Congenital Hypothyroidism (CH) Patient 1812


title: Congenital Hypothyroidism (CH) Patient 5008


title: Congenital Hypothyroidism (CH) Patient 2672


title: Congenital Hypothyroidism (CH) Patient 3223


title: Congenital Hypothyroidism (CH) Patient 2413


title: Congenital Hypothyroidism (CH) Patient 1436


title: Congenital Hypothyroidism (CH) Patient 4655


title: Congenital Hypothyroidism (CH) Patient 3242


title: Congenital Hypothyroidism (CH) Patient 2824


title: Congenital Hypothyroidism (CH) Patient 2969


title: Congenital Hypothyroidism (CH) Patient 1829


title: Congenital Hypothyroidism (CH) Patient 3738


title: Congenital Hypothyroidism (CH) Patient 4664


title: Congenital Hypothyroidism (CH) Patient 2315


title: Congenital Hypothyroidism (CH) Patient 1937


title: Congenital Hypothyroidism (CH) Patient 2371


title: Congenital Hypothyroidism (CH) Patient 1655


title: 24hr replicate 2

city: Charleston

first: Jimmy

middle: C

last: Ryan

state: SC

address: 331 Fort Johnson Rd

department: Marine Biotoxins

institute: NOAA

description: 24hr positive polarity

hyb_protocol: 17 hrs, 60 degrees C according to Agilent protocol in Agilent recommended hyb oven

scan_protocol: Agilent B Scanner (Agilent Technologies Scanner G2505B US22502617)

data_processing: Data extracted with Agilent Feature Extraction software version A8.5.3, and data analyzed with Rosetta Resolver 7.0 gene expression analysis system (Rosetta Informatics, Seattle, WA).

source_name: control brain

label_protocol: Agilent low input amplification kit, 500ng input

growth_protocol: 12:12 light dark cycle animal facilities

extract_protocol: Total RNA extracted with Trizol and Rneasy Clean up

treatment_protocol: Treated with Pacific ciguatoxin

value: Brain

value: untreated

tag: time

source_name: treated brain

value: ciguatoxin


title: 1hr replicate 3

description: 1hr negative polarity

tag: agent

value: control


title: Congenital Hypothyroidism (CH) Patient 1622


title: Congenital Hypothyroidism (CH) Patient 1592


title: Untreated cells lan5_rep2

status: Public on May 31 2010

city: Rome

first: camilla

last: bernardini

address: L.go F.Vito 1

department: Human Anatomy

country: Italy

institute: UCSC

description: untreated cells lan5

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-Focus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Raw data have been normalized using gc-RMA methods

source_name: Lan5 commercial cell line

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

growth_protocol: cells were cultured in complete DMEM till 80% confluence, then placed at 60000 cells per squared cm

extract_protocol: Rneasy mini kit extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: no treatment (cells treated with cell culture medium alone)

value: neuroblastoma


title: 4hr replicate 3

description: 4hr negative polarity


title: Congenital Hypothyroidism (CH) Patient 1796

value: female


title: Congenital Hypothyroidism (CH) Patient 2625


title: Congenital Hypothyroidism (CH) Patient 1973


title: 24hr replicate 1

description: 24hr positive polarity


title: Congenital Hypothyroidism (CH) Patient 1830


title: 4hr replicate 2

description: 4hr negative polarity


title: 2008 cells_rep3

first: Meghan

last: Verschoor

state: Ontario

address: 699 Concession St

department: Medical Sciences

country: Canada

institute: McMaster University

description: Tetracycline induced, 24hrs

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized on GeneChip Human Gene 1.0ST Array (Lot# 4067343). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with R version 2.9.2. Background correction and normalization was performed using the robust multi-array average (RMA) algorithm.

source_name: 2008 ovarian cancer cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix WT Kit from 300ng total RNA

growth_protocol: RPMI +10% FBS + 1% PenStrep (2008), RPMI +10% FBS + 1% PenStrep + 100ug/ml Zeocin (2008-Ets1)

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen), DNase treated with Turbo DNA-free (Ambion), and cleaned up using RNeasy columns (Qiagen)

treatment_protocol: Induced with tetracycline (2ug/ml) over 24 hours prior to RNA isolation

value: ovarian cancer

tag: ets-1 expression status (western blot)

value: No detectable Ets-1 protein expression


title: 2008-Ets1 cells_rep3

description: Tetracycline induced, 24hrs

source_name: 2008-Ets1 stable inducible (tetracycline) ovarian cancer cells

value: High levels of Ets-1 protein expression


title: 4hr replicate 1

description: 4hr positive polarity


title: 1hr replicate 2

description: 1hr negative polarity


title: 24hr replicate 3

description: 24hr negative polarity


title: 2008-Ets1 cells_rep2

description: Tetracycline induced, 24hrs


title: Congenital Hypothyroidism (CH) Patient 4614


title: 2008-Ets1 cells_rep1

description: Tetracycline induced, 24hrs


title: 2008 cells_rep2

description: Tetracycline induced, 24hrs


title: Untreated cells Lan5_rep3

description: untreated cells lan5


title: Lan5_s100b_5uM_rep3

description: treated cells lan5 s100b 5uM

treatment_protocol: s100b 5uM


title: Lan5_s100b_5uM_rep2

description: treated cells lan5 s100b 5uM


title: Lan5_s100b_5uM_rep1

description: treated cells lan5 s100b 5uM


title: Lan5_s100b_0.5nM_rep2

description: treated cells lan5 s100b 0.5nM


title: Lan5_s100b_0.5nM_rep3

description: treated cells lan5 s100b 0.5nM


title: 2008 cells_rep1

description: Tetracycline induced, 24hrs


title: Untreated cells lan5_rep1

description: untreated cells lan5


title: Primary Lung Adenocarcinoma_Sample_A61

status: Public on May 28 2010

first: Jill

middle: Everland

last: Larsen

address: Rode Road, Chermside

department: Thoracic Medicine

institute: The Prince Charles Hospital

hyb_protocol: After the purification, the samples were combined for hybridization. The labeled cDNAs were co-hybridized to 22K oligo microarrays.

scan_protocol: Slides were scanned on a GMS418 confocal scanner (Agilent).

data_processing: Raw images were imported into Imagene V5.1 (BioDiscovery, CA, USA) to extract pixel intensities and to flag spots with poor/absent signal. The raw background-subtracted signal median for each probe was imported into GeneSpring GX V7.3 (Agilent Technologies, Inc., CA, USA) for analysis. Data was normalized (Lowess: per spot and per chip; per chip to the 50th percentile) and probe signals filtered on pixel intensity (for both red and green channels any spots less than 20 units or greater than 65,000 units were excluded) and consistent spot morphology. Only spots flagged present in at least 80% of samples were included. For each probe, the logarithm to the base 2 of the ratio between the intensity in the tumor sample (red) channel and the reference (green) channel was used as the expression value for the probe.

source_name: Universal Reference RNA

label_protocol: Synthesis of the labelled first strand cDNA was conducted using Amersham CyScribe Post-Labelling kit with starting material of 20 ug of total RNA. The amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA probes were purified using Amersham GFX columns. Dye coupling reactions were performed by mixing the cDNA samples with Amersham Cy3 (reference) or Cy5 (tumour) and incubating in the dark. The reactions were purified with Amersham GFX columns to remove the unincorporated/quenched dyes.

extract_protocol: The Universal Reference RNA was commercially available (Stratagene).

value: pool of 10 cell lines

value: reference

source_name: Tumour sample A61, NARLC-AC

extract_protocol: Total RNA was extracted from fresh-frozen tissue using Trizol (Invitrogen) and RNeasy (Qiagen) clean-up.

value: primary lung adenocarcinoma

tag: lung cancer type

value: non-asbestos-related lung cancer-adenocarcinoma (NARLC-AC)

tag: age (yrs)


title: cells

status: Public on May 21 2010

city: Adelaide

first: Anna

last: Tsykin

state: SA

address: Frome Road

department: Hanson Institute

institute: SA Pathology

description: no additional information

hyb_protocol: hybridysed at Adelaide Microarray Facility http://www.microarray.adelaide.edu.au/

scan_protocol: Slides were scanned with a GenePix 4000B Scanner (Axon Instruments)

data_processing:
Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Morphological opening background correction was applied to mean spot signal intensities. Analysis was performed in R with LIMMA package of BioConductor. Intensity-dependent global loess normalization was applied and the linear model fitted.
VALUE = normalized log2 ratio (Cy5/Cy3)

label_protocol: miRNA was labeled by RNA-ligase mediated ligation of Cy dye-coupled dinucleotides.

growth_protocol: Cells were grown in F12 medium containing 5% charcoal stripped fetal bovine serum (lonza) containing 10 nM beta-estradiol

extract_protocol: RNA was extracted with miRNeasy minikit (Qiagen).

treatment_protocol: logarithmically growing cells were cultured in the presence or absence of 1 micromolar all-trans retinoic acid for 6 or 48 hours. At the end of the experiment total RNA, containing the microRNA fraction, was extracted and used for miR and GX profiling

value: 6 hours


title: Primary Lung Adenocarcinoma_Sample_A68

city: Brisbane

tag: sample type

source_name: Tumour sample A68, ARLC-AC

value: asbestos-related lung cancer-adenocarcinoma (ARLC-AC)

value: male


title: Primary Lung Adenocarcinoma_Sample_A70

source_name: Tumour sample A70, ARLC-AC


title: Primary Lung Adenocarcinoma_Sample_A62

source_name: Tumour sample A62, ARLC-AC


title: - cells - RA.cells

description: no additional information

value: RA treated


title: Lan5_s100b_0.5nM_rep1

description: treated cells lan5 s100b 0.5nM

tag: cell type


title: Primary Lung Adenocarcinoma_Sample_A69

source_name: Tumour sample A69, ARLC-AC


title: Primary Lung Adenocarcinoma_Sample_A66

source_name: Tumour sample A66, ARLC-AC


title: - cells - RA.cells - cells.time - RA.cells.time

description: no additional information

value: 48 hours


title: - cells

description: no additional information

value: untreated


title: Primary Lung Adenocarcinoma_Sample_A56

source_name: Tumour sample A56, ARLC-AC


title: Primary Lung Adenocarcinoma_Sample_A60

source_name: Tumour sample A60, ARLC-AC


title: Primary Lung Adenocarcinoma Sample_A50

source_name: Tumour sample A50, NARLC-AC


title: Primary Lung Adenocarcinoma_Sample_A54

source_name: Tumour sample A54, NARLC-AC


title: Primary Lung Adenocarcinoma Sample_A7

source_name: Tumour sample A7, NARLC-AC


title: Primary Lung Adenocarcinoma_Sample_A59

source_name: Tumour sample A59, ARLC-AC


title: Primary Lung Adenocarcinoma_Sample_A55

source_name: Tumour sample A55, ARLC-AC


title: - cells - cells.time

description: no additional information


title: cells + RA.cells

description: no additional information


title: Primary Lung Adenocarcinoma_Sample_A67

source_name: Tumour sample A67, NARLC-AC


title: cells + RA.cells + cells.time + RA.cells.time

description: no additional information


title: cells + cells.time

description: no additional information


title: - RA - RA.cells

description: no additional information


title: RA + RA.time + RA.cells + RA.cells.time

description: no additional information


title: - RA  - RA.time - RA.cells - RA.cells.time

description: no additional information


title: RA + RA.cells

description: no additional information


title: time + cells.time

description: no additional information


title: RA + RA.time

description: no additional information


title: time + RA.time + cells.time + RA.cells.time

description: no additional information


title: - time

description: no additional information


title: - RA

description: no additional information


title: - time - RA.time - cells.time - RA.cells.time

description: no additional information


title: RA

description: no additional information


title: - RA - RA.time

description: no additional information


title: time

description: no additional information


title: time + RA.time

description: no additional information


title: - time - RA.time

description: no additional information


title: - time - cells.time

description: no additional information


title: Labeled MSCs 24 P4 Pulsin (MSC labeling Chip20)

status: Public on May 17 2010

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

description: Slides were scanned in a microarray scanner (Genetix Limited, Hampshire, UK). Photomultiplier tube voltage was set to 100% for both red and green channels. The two resulting green and red images were overlaid using ImaGene 5 (BioDiscovery, Inc., CA, USA).

hyb_protocol: Pre-hybridization Note: Do not allow the slides to dry during the pre-hybridization and washing procedure. 1. Pre-warm an appropriate volume of Nexterion 70mer Oligo Pre-Hyb to 48°C for 10 minutes until the precipitate is completely dissolved. 2. Incubate slides in Nexterion 70mer Oligo Pre-Hyb for 45 min at 48°C. Use a large enough volume of buffer to ensure that all slides are completely covered with Nexterion Pre-Hyb. 3. During the pre-hybridization step, prepare Wash Solution 1 by diluting Nexterion 70mer Oligo Wash B 1:40 with diH2O. Prepare 50 ml per slide (i.e. 1.25 ml Nexterion 70mer Oligo Wash B, add diH2O to 50 ml). 4. Wash 5 min in Wash Solution 1 at 20 to 25°C. 5. Rinse with diH2O for 30 sec. 6. Dry the Nexterion Slide E with nitrogen. Hybridization Prewarm Hybsolution 15 minutes before hybridization at 68°C. Clean coverslips with dH20 and 100% Ethanol and dry the coverslips with nitrogen. 1. Pipette 40µl of hybridization to the solution. Denature the fragmented target in the hyb-buffer by heating at 95°C for 3 min. Then let the probe cool down for 1 min at RT. Afterwards place the target onto the array surface of a prehybridized slide under the coverslip 3. Hybridize the slide at 48°C for 16 hours. Post-hybridization washing Note: Do not allow the slides to dry during the hybridization and washing procedure. Wash Solution 2, 3 and 4 should be prepared in advance. Use at least 50 ml solution per slide. Post-hybridization washing solutions: Preparation: Wash Solution 2: 50 ml Nexterion 70mer Oligo Wash A, 25 ml Nexterion 70mer Oligo Wash B, Make up to 500 ml with diH2O Wash Solution 3: 50 ml Nexterion 70mer Oligo Wash A, Make up to 500 ml with diH2O Wash Solution 4: 5 ml Nexterion 70mer Oligo Wash A, Make up to 500 ml with diH2O 1. Place the array into a slide rack and immerse in a dish containing Wash Solution 2. Wash in the above solution 1 x 10 min at 20 to 25°C. 2. Wash 1 x 10 min in Wash Solution 3 at 20 to 25°C. 3. Wash 1 x 10 min in Wash Solution 4 at 20 to 25°C. 4. Dry the array with nitrogen. 5. Protect the array from light, dust and abrasion of the array surface, until ready for scanning.

scan_protocol: not further description needed

data_processing: The data was normalized using median normalization on the normexp-background corrected expression values, followed by a  in-between-array quantile normalization. Both the median and quantile normalization methods were used as provided in the limma package.

source_name: Unlabeled control 24 P4

label_protocol: Amino Allyl MessageAmp II aRNA Amplification Kit performed according to the provided manual

extract_protocol: Machery & Nagel RNA extraction kit performed according to the provided manual

value: Mesenchymal stem cells not labeled with ferritin, cell line 24, passage P4

value: Mesenchymal stem cells

source_name: Labeled MSCs 24 P4 Pulsin

value: Mesenchymal stem cells labeled with ferritin Pulsin, cell line 24, passage P4

value: Pulsin


title: Labeled MSCs 24 P4 dosper (MSC labeling Chip18)

value: control

source_name: Labeled MSCs 24 P4 dosper

value: Mesenchymal stem cells labeled with ferritin dosper, cell line 24, passage P4

value: dosper


title: Labeled MSCs 24 P4 R60 (MSC labeling Chip16)

source_name: Labeled MSCs 24 P4 R60

value: Mesenchymal stem cells labeled with ferritin R60, cell line 24, passage P4


title: Labeled MSCs 24 P4 jetpei (MSC labeling Chip19)

source_name: Labeled MSCs 24 P4 jetpei

value: Mesenchymal stem cells labeled with ferritin jetpei, cell line 24, passage P4

value: jetpei


title: Labeled MSCs 24 P2 Pulsin (MSC labeling Chip15)

source_name: Unlabeled control 24 P2

value: Mesenchymal stem cells not labeled with ferritin, cell line 24, passage P2

source_name: Labeled MSCs 24 P2 Pulsin

value: Mesenchymal stem cells labeled with ferritin Pulsin, cell line 24, passage P2


title: Labeled MSCs 24 P4 R200 (MSC labeling Chip17)

source_name: Labeled MSCs 24 P4 R200

value: Mesenchymal stem cells labeled with ferritin R200, cell line 24, passage P4


title: MCF7 cells, retinoic acid effect, time 48h, repl1

city: Milano

first: Maddalena

last: Fratelli

address: Via La Masa, 19

institute: "Mario Negri" Institute

description: Biological replicates 1 of 2

hyb_protocol: hybridization and washing were done according to Agilent protocol (GE version 5.5 )

scan_protocol: Agilent Technologies Scanner G2505B US45102933,  5 micron resolution and XDR protocol, using the Agilent scan control software.

data_processing: Image data analysis was performed using the Feature extraction software (v9.1). The raw data FE files report log10 (Cy5/Cy3) ratios. Detailed description of the protocols used is reported in each raw data file. LogRatios are derived by Lowess normalizatin of Median Signals (maNorm function of marray package in Bioconductor).

source_name: MCF7 cells, untreated, time 48h, repl1

label_protocol: Amino Allyl cDNA Labeling Kit (cat 1705, Ambion), following manufacturer's instructions. Samples were then diluted 1:10 and 15 picomoles of each dye were used for hyhbridization

growth_protocol: Cells were grown in F12  medium containing 5% charcoal stripped fetal bovine serum (lonza) containing 10 nM beta-estradiol

extract_protocol: total RNA extracted using Qiagen miRNeasy kit, followed by Rneasy MinElute Cleanup, following manufacturer's instructions

treatment_protocol: logarithmically growing cells were cultured in the presence or absence of 1 micromolar all-trans retinoic acid for 6 or 48 hours.  At the end of the experiment total RNA, containing the microRNA fraction, was extracted and used for miR and GX profiling

value: Vehicle

source_name: MCF7 cells, retinoic acid treated, time 48h, repl1

value: 1 microM Retinoic Acid


title: MDA-MB-231  cells, retinoic acid effect, time 6h, repl1

description: Biological replicates 1 of 2

source_name: MDA-MB-231 cells, untreated, time 6h, repl1

value: 6 hours

source_name: MDA-MB-231 cells, retinoic acid treated, time 6h, repl1


title: MDA-MB-231  cells, retinoic acid effect, time 6h, repl2

description: Biological replicates 2 of 2

source_name: MDA-MB-231 cells, retinoic acid treated, time 6h, repl2

source_name: MDA-MB-231 cells, untreated, time 6h, repl2


title: MDA-MB-231  cells, retinoic acid effect, time 48h, repl1

description: Biological replicates 1 of 2

source_name: MDA-MB-231 cells, untreated, time 48h, repl1

value: 48 hours

source_name: MDA-MB-231 cells, retinoic acid treated, time 48h, repl1


title: MCF7 cells, retinoic acid effect, time 6h, repl2

description: Biological replicates 2 of 2

source_name: MCF7 cells, retinoic acid treated, time 6h, repl2

source_name: MCF7 cells, untreated, time 6h, repl2


title: Labeled MSCs 21 P4 dosper (MSC labeling Chip8)

source_name: Unlabeled control 21 P4

value: Mesenchymal stem cells not labeled with ferritin, cell line 21, passage P4

source_name: Labeled MSCs 21 P4 dosper

value: Mesenchymal stem cells labeled with ferritin dosper, cell line 21, passage P4


title: Labeled MSCs 24 P2 R200 (MSC labeling Chip12)

value: Mesenchymal stem cells

source_name: Labeled MSCs 24 P2 R200

value: Mesenchymal stem cells labeled with ferritin R200, cell line 24, passage P2


title: MCF7 cells, retinoic acid effect, time 48h, repl2

description: Biological replicates 2 of 2

source_name: MCF7 cells, retinoic acid treated, time 48h, repl2

source_name: MCF7 cells, untreated, time 48h, repl2


title: Labeled MSCs 21 P4 R60 (MSC labeling Chip6)

value: control

source_name: Labeled MSCs 21 P4 R60

value: Mesenchymal stem cells labeled with ferritin R60, cell line 21, passage P4


title: Labeled MSCs 21 P4 R200 (MSC labeling Chip7)

source_name: Labeled MSCs 21 P4 R200

value: Mesenchymal stem cells labeled with ferritin R200, cell line 21, passage P4


title: Labeled MSCs 24 P2 R60 (MSC labeling Chip11)

source_name: Unlabeled control 24 P2

source_name: Labeled MSCs 24 P2 R60

value: Mesenchymal stem cells labeled with ferritin R60, cell line 24, passage P2


title: 1hr replicate 1

description: 1hr positive polarity

source_name: control brain

value: Brain

value: untreated

source_name: treated brain

value: ciguatoxin


title: Labeled MSCs 21 P4 jetpei (MSC labeling Chip9)

source_name: Labeled MSCs 21 P4 jetpei

value: Mesenchymal stem cells labeled with ferritin jetpei, cell line 21, passage P4

value: jetpei


title: Labeled MSCs 21 P2 Pulsin (MSC labeling Chip5)

source_name: Unlabeled control 21 P2

value: Mesenchymal stem cells not labeled with ferritin, cell line 21, passage P2

source_name: Labeled MSCs 21 P2 Pulsin

value: Mesenchymal stem cells labeled with ferritin Pulsin, cell line 21, passage P2

value: Pulsin


title: Labeled MSCs 21 P4 Pulsin (MSC labeling Chip10)

source_name: Labeled MSCs 21 P4 Pulsin

value: Mesenchymal stem cells labeled with ferritin Pulsin, cell line 21, passage P4


title: Labeled MSCs 21 P2 dosper (MSC labeling Chip3)

source_name: Labeled MSCs 21 P2 dosper

value: Mesenchymal stem cells labeled with ferritin dosper, cell line 21, passage P2

value: dosper


title: MDA-MB-231  cells, retinoic acid effect, time 48h, repl2

description: Biological replicates 2 of 2

source_name: MDA-MB-231 cells, retinoic acid treated, time 48h, repl2

value: 1 microM Retinoic Acid

value: 48 hours

source_name: MDA-MB-231 cells, untreated, time 48h, repl2

value: Vehicle


title: MCF7 cells, retinoic acid effect, time 6h, repl1

description: Biological replicates 1 of 2

source_name: MCF7 cells, untreated, time 6h, repl1

value: 6 hours

source_name: MCF7 cells, retinoic acid treated, time 6h, repl1


title: Labeled MSCs 21 P2 jetpei (MSC labeling Chip4)

value: Mesenchymal stem cells

value: control

source_name: Labeled MSCs 21 P2 jetpei

value: Mesenchymal stem cells labeled with ferritin jetpei, cell line 21, passage P2


title: Labeled MSCs 21 P2 R60 (MSC labeling Chip1)

source_name: Labeled MSCs 21 P2 R60

value: Mesenchymal stem cells labeled with ferritin R60, cell line 21, passage P2


title: Labeled MSCs 21 P2 R200 (MSC labeling Chip2)

source_name: Labeled MSCs 21 P2 R200

value: Mesenchymal stem cells labeled with ferritin R200, cell line 21, passage P2


title: Labeled MSCs 24 P2 dosper (MSC labeling Chip13)

value: Mesenchymal stem cells not labeled with ferritin, cell line 24, passage P2

source_name: Labeled MSCs 24 P2 dosper

value: Mesenchymal stem cells labeled with ferritin dosper, cell line 24, passage P2


title: Proband 7 6h (Clock Genes Chip26)

scan_protocol: not further discription needed

source_name: Reference

extract_protocol: Universal Human Reference RNA, Stratagene

value: global Reference

source_name: Proband 7 6h

value: oral mucosa

tag: individual

value: proband 7


title: Proband 8 18h (Clock Genes Chip32)

source_name: Proband 8 18h

tag: tissue

value: proband 8


title: Proband 8 6h (Clock Genes Chip30)

source_name: Proband 8 6h


title: Proband 7 12h (Clock Genes Chip27)

source_name: Proband 7 12h


title: Proband 7 18h (Clock Genes Chip28)

source_name: Proband 7 18h


title: Proband 6 18h (Clock Genes Chip24)

source_name: Proband 6 18h

value: proband 6


title: Proband 6 12h (Clock Genes Chip23)

source_name: Proband 6 12h


title: Proband 5 18h (Clock Genes Chip20)

source_name: Proband 5 18h

value: proband 5


title: Proband 6 0h (Clock Genes Chip21)

source_name: Proband 6 0h


title: Proband 5 6h (Clock Genes Chip18)

source_name: Proband 5 6h


title: Proband 6 6h (Clock Genes Chip22)

source_name: Proband 6 6h


title: Proband 5 12h (Clock Genes Chip19)

source_name: Proband 5 12h


title: Proband 5 0h (Clock Genes Chip17)

source_name: Proband 5 0h


title: Proband 7 0h (Clock Genes Chip25)

source_name: Proband 7 0h


title: Proband 4 0h (Clock Genes Chip13)

source_name: Proband 4 0h

value: proband 4


title: Proband 3 18h (Clock Genes Chip12)

source_name: Proband 3 18h

value: proband 3


title: Proband 4 6h (Clock Genes Chip14)

source_name: Reference

source_name: Proband 4 6h


title: Proband 3 12h (Clock Genes Chip11)

source_name: Proband 3 12h


title: Proband 3 0h (Clock Genes Chip9)

source_name: Proband 3 0h


title: Proband 2 18h (Clock Genes Chip8)

source_name: Proband 2 18h

value: proband 2


title: Proband 3 6h (Clock Genes Chip10)

source_name: Proband 3 6h


title: Proband 2 12h (Clock Genes Chip7)

source_name: Proband 2 12h


title: Proband 8 0h (Clock Genes Chip29)

source_name: Proband 8 0h


title: Proband 2 6h (Clock Genes Chip6)

source_name: Proband 2 6h


title: Proband 4 18h (Clock Genes Chip16)

source_name: Proband 4 18h


title: Proband 4 12h (Clock Genes Chip15)

source_name: Proband 4 12h


title: Medium 24h (Lactate HUVEC Chip10)

status: Public on May 16 2010

source_name: Medium 24h

value: Medium

value: HUVECs


title: Lactate 24h (Lactate HUVEC Chip9)

source_name: Lactate 24h

value: Lactate


title: Proband 1 6h (Clock Genes Chip2)

source_name: Proband 1 6h

value: proband 1


title: Proband 2 0h (Clock Genes Chip5)

source_name: Proband 2 0h


title: Proband 1 18h (Clock Genes Chip4)

source_name: Proband 1 18h


title: Medium 16h (Lactate HUVEC Chip8)

source_name: Medium 16h


title: Lactate 16h (Lactate HUVEC Chip7)

source_name: Reference

source_name: Lactate 16h


title: Medium 8h (Lactate HUVEC Chip6)

source_name: Medium 8h


title: Proband 1 0h (Clock Genes Chip1)

source_name: Proband 1 0h


title: Lactate 8h (Lactate HUVEC Chip5)

source_name: Lactate 8h


title: Medium 1h (Lactate HUVEC Chip2)

source_name: Medium 1h


title: Lactate 4h (Lactate HUVEC Chip3)

source_name: Lactate 4h


title: Lactate 1h (Lactate HUVEC Chip1)

source_name: Lactate 1h


title: Labeled MSCs 24 P2 jetpei (MSC labeling Chip14)

source_name: Unlabeled control 24 P2

value: Mesenchymal stem cells

value: control

source_name: Labeled MSCs 24 P2 jetpei

value: Mesenchymal stem cells labeled with ferritin jetpei, cell line 24, passage P2

value: jetpei


title: Proband 1 12h (Clock Genes Chip3)

value: global Reference

source_name: Proband 1 12h