title: light zone, biological replicate 1

description: Gene expression data from sorted B cells photoactivated in the GC light zone

source_name: day 7 germinal center light zone cells


title: naive, biological replicate 1

status: Public on Sep 07 2010

type: RNA

city: Cambridge

first: Gabriel

middle: D

last: Victora

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute

description: Gene expression data from naïve (IgD+) B cells from spleen

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse MOE 430 2.0 gene chips. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned on Affymetrix GeneChip Scanner 3000 using AGCC 2.0 Software

data_processing: The data were analyzed with GeneSpring 11 using Affymetrix default analysis settings and RMA as normalization method.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: naïve splenic B cells

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3'IVT Express Kit.

growth_protocol: Germinal centers were induced by immunization with ovalbumin in alum followed by transfer of PA-GFP+ B1-8hi B cells and boosting with soluble NP-ovalbumin

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

treatment_protocol: Cells were photoactivated in the dark or light zones of intact lymph nodes and sorted by flow cytometry

tag: tissue

value: spleen

tag: cell type

value: naive B cells


title: Patient 3

status: Public on Sep 06 2010

city: Boston

first: Richelle

middle: C.

last: Charles

address: 55 Fruit Street, Gray 504

department: Infectious Diseases

institute: Massachussetts General Hospital

description: Analysis used in vitro RNA as control samples for comparison to the in vivo samples.

hyb_protocol: Labeled products were added to activated Salmonella ORF microarray glass slides (version STv7S; McClelland Laboratory, Vaccine Research Institute of San Diego, CA, http://www.sdibr.org/Faculty/mcclelland/mcclelland-lab), and developed as previously described (Larocque RC et. al. (2005). Infect Immun 73: 4488-4493 [PMID 16040959]).

scan_protocol: Arrays were scanned using a Perkin Elmer scanner and ScanArray Express software version 4.

data_processing: For analyses, we subtracted local background from spot signal intensities, and considered a cDNA for an ORF detected in a particular sample if it met the following criteria: 1) the median signal intensity of at least 2 of its 3 replicate spots on the array was at least ten median absolute deviations greater than the median of spots on the microarray corresponding to genes absent from the S. Paratyphi A genome, and 2) this criteria was met on greater than 75% of slides for that subject.  We then evaluated differences in expression in in vitro versus in vivo grown organisms for all genes detected in in vivo samples.  Using LOESS-normalized, log-transformed data, we employed repeated measures ANOVA (to within slide replicate spots) with fixed type (in vivo versus in vitro) and dye effects with Benjamini-Hochberg correction.  We only considered array features with a coefficient of variation in signal intensity of less than 50% within an array.  We considered significant variations in signal intensity as determined by ANOVA indication of potentially differentially expressed genes.  Since the samples were hybridized to two-channel arrays, the data from different slides were not normalized to have the same median intensities. Instead we used a simple (standard) method of analysis described by Kerr et. al (2001) Genetics Research, 77:123-128 (PMID 11355567) which included a slide effect in the analysis of variance model. Thus, for each gene when comparing in vivo and in vitro levels, the slide effect was adjusted for in the model fit, and there was no need to normalize data to have same median intensities across the slides.

organism: Salmonella enterica subsp. enterica serovar Paratyphi A

source_name: in vitro

label_protocol: We differently labeled in vivo and in vitro SCOTS-cDNAs for each of three patients with S. Paratyphi A bacteremia (Dziejman et. al. (2002) PNAS, 99: 1556-1561 [PMID 11818571]).

growth_protocol: To create cDNA of organisms in the blood of bacteremic patients (in vivo samples), we used TRIzol-preserved blood samples of patients whose day 0 culture subsequently grew S. Paratyphi A.  To generate corresponding in vitro cDNA samples, we grew each patient's bacterial isolate in Luria Bertani (LB) broth until mid-log growth phase (OD600 0.45-0.6), and then immediately placed these samples into TRIzol at a 1 (mid-log culture):2 (TRIzol) volume ratio.

extract_protocol: We recovered total RNA from TRIzol-preserved in vivo and in vitro samples per manufacturer's instructions (Invitrogen), and treated with DNase on RNeasy columns (Qiagen).  We converted 5 µg of total extracted RNA into cDNA using random priming (T-PCR) to obtain a representative cDNA population as described by Froussard (Froussard P. 1992. Nucleic Acids Res 20: 2900 [PMID 1614887]), with modifications as previously described by Graham (Graham JE. 1999. PNAS. 96: 11554-11559 [PMID 10500215]).  We performed three rounds of SCOTS on in vivo and in vitro cDNA samples, as previously described (Graham JE. 1999. PNAS. 96: 11554-11559 [PMID 10500215]).

tag: serovar

value: Paratyphi A

tag: growth condition

value: in vitro (LB media)

tag: patient

source_name: in vivo

value: in vivo (blood of bacteremic patient)


title: Hsa embryos 14 wga N1

city: Miami

first: Ricardo

last: Pastori

state: FL

department: Diabetes Research Institute

institute: University of Miami

description: The embryonic human pancreas were embeded in 10% volume of RNAlater solution (Ambion).

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
Data was processed using the softwares SDS 2.3 and RQ manager 1.2 from Applied Biosystems.
dCt for delta Ct, defined by the formula (Ct of the specific miRNA-Ct of the endogenous control RNU48) for each sample. RQ for relative quantification, defined by the formula 2^-dCt . Small nuclear RNA (RNU48) was used as endogenous control.

label: FAM

organism: Homo sapiens

source_name: embryonic human pancreas

label_protocol: standard Taqman assay

extract_protocol: Total RNA was isolated using the miRVana microRNA isolation kit (Ambion).

tag: gestational age

value: 14 wk

value: embryonic pancreas


title: Patient 3, replicate


title: Clark 10DAP, Fe sufficient, biological rep 2

city: St. Paul

first: Carroll

middle: P

last: Vance

state: MN

address: 1991 Upper Buford Circle, 411 Borlaug Hall

department: Agronomy and Plant Genetics

institute: USDA-ARS, University of Minnesota

description: Gene expression data from iron sufficient Clark 10DAP

hyb_protocol: RNA samples were submited to the University of Minnesota BioMedical Genomics Centerfor hybridization to Soybean Affymetrix GeneChips

scan_protocol: GeneChips were scanned using the Genechip 3000 scanner

data_processing: Data was analyzed using the 'justRMA' command in R.  Data was analyzed for  10DAP roots and 14DAP roots

organism: Glycine max

source_name: Clark 10 day roots, Fe sufficient, biological rep 2

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

growth_protocol: seeds were germinated on germination paper in growth chambers for 1 week.  Seedlings were transferred to hydroponic solutions of 2mM MgSO4*7H2O, 3mM Mg(NO3)2*6H2O, 2.5mM KNO3, 1mM CaCL2*2H2O, 4mM Ca(NO3)2*4H2O, 0.020mM KH2PO4, 542uM KOH, 217uM DTPA, 1.5uM MnCl2 *4H2O, 4.6uM ZnSO4*7H2O, 2uM CuSO4*5H2O, 0.2uM NaMoO4*2H2O, 1uM CoSO4*7H2O, 1uM NiSO4*6H2O, 10uM H3BO3, 20mM HCO3, and either 50 or 100uM Fe(NO3)3.  A daily nutrient solution of 16mM KPO4, 0.287mM H3BO3, and 355mM NH4(NO3)3 maintained stable nutrient conditions.

extract_protocol: RNA was extracted using the TRIzol method, DNAse treated with Ambion DNA-free kit, then further purified using the RNeasy mini kit (QIAGEN)

treatment_protocol: plants were grown in either iron sufficient (100uM Fe(NO3)3) or iron limited (50uM Fe(NO3)3) hydroponic conditions.  After 10 days, the roots of half the plants were collected in liquid nitrogen.  12 days after planting, Iron was added to all remaining hydroponic solutions to either bring the iron levels up to iron sufficient conditions or maintain iron sufficient growth conditions.  14 days after planting, the remaining plant roots were harvested in liquid nitrogen.

tag: isogenic line

value: Clark

tag: time point

value: 10 days

tag: condition

value: Fe sufficient

tag: biological replicate

value: Total Roots


title: Clark 10DAP, Fe sufficient, biological rep 1

source_name: Clark 10 day roots, Fe sufficient, biological rep 1


title: Clark 10DAP, Fe limited, biological rep 3

description: Gene expression data from iron deficient Clark 10DAP

source_name: Clark 10 day roots, Fe limited, biological rep 3

value: Fe limited


title: Hsa embryos 11 wga

value: 11 wk


title: Hsa embryos 13 wga

value: 13 wk


title: dark zone, biological replicate 1

description: Gene expression data from sorted B cells photoactivated in the GC dark zone

source_name: day 7 germinal center dark zone cells

value: lymph node

value: germinal center B cells


title: Hsa embryos 10 wga N2

value: 10 wk


title: Control B, dye reversal

description: Analysis used in vitro RNA with SCOTS as control samples for comparison to the in vitro samples prepared without SCOTS.

source_name: in vitro without SCOTS

tag: scots

value: no

tag: sample type

value: control

source_name: in vitro with SCOTS

value: yes


title: Patient 2, replicate

value: Paratyphi A

value: in vitro (LB media)


title: Patient 3, dye reversal

value: in vivo (blood of bacteremic patient)


title: Patient 3, dye reversal, replicate


title: Control A


title: Hsa embryos 10 wga N1

value: embryonic pancreas


title: Control A, replicate


title: Patient 2, dye reversal


title: Patient 2


title: Clark 10DAP, Fe limited, biological rep 2

source_name: Clark 10 day roots, Fe limited, biological rep 2

value: Clark


title: SCARKO-jsd_testis_rep2

city: Houston

first: JoAnne

last: Richards

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: gene expression data

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

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

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

source_name: testis from SCARCO-jsd mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

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

value: testis

tag: genotype

value: SCARO-jsd

tag: age

value: 12 weeks


title: Clark 14DAP, Fe sustained, biological rep 2

description: Gene expression data from iron sufficiency sustained Clark 14 DAP

source_name: Clark 14 day roots, Fe sufficient, biological rep 2

value: 14 days

value: Fe sufficient

value: Total Roots


title: light zone, biological replicate 2

value: lymph node


title: Iso 10DAP, Fe sufficient, biological rep 2

description: Gene expression data from iron sufficient IsoClark 10DAP

source_name: IsoClark 10 day roots, Fe sufficient, biological rep 2

value: IsoClark

value: 10 days


title: Control group, replicate 2

city: Singapore

first: George

middle: W

last: Yip

address: 4 Medical Drive, Block MD10

country: Singapore

institute: National University of Singapore

description: Gene expression data from MDA-MB-231 cells transfected with negative control pre-miRNA

hyb_protocol: Fragmented cRNA was hybridised at 45°C for 16 hours to Affymetrix HG U133 Plus 2.0 GeneChips, followed by washing and staining in an Affymetrix FS450 fluidics station.

scan_protocol: GeneChips were scanned using a GCOS 7000 7G scanner.

data_processing: Data were analysed using GeneSpring GX11.0 with RMA normalisation to median signal intensity.

label_protocol: Biotinylated cRNA was prepared according th the standard Affymetrix protocol from 2.9 μg of total RNA.

growth_protocol: MDA-MB-231 cells were cultured at 37°C in a humidified atmosphere with 5% carbon dioxide.

extract_protocol: Total RNA extracted using the Qiagen RNeasy Kit.

treatment_protocol: Cells were transfected with pre-miR-145 or a negative control pre-miRNA.

value: Breast cancer cells

value: MDA-MB-231 cells


title: Endometrium-d2-3- pregnant 1

city: Brussel

first: Inge

last: Van Vaerenbergh

address: Laarbeeklaan 103

department: EXPA

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Hybridized overnight to the Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix)

scan_protocol: Scanned on a 2-µm Affymetrix 3000 GeneScanner

data_processing: Affymetrix GeneChip Operating (GCOS) 1.2 was used to analyze the resulting image files. The global scaling technique was used to scale the fluorescence intensity of each chip to a target signal of 150.

source_name: Endometrium on day of oocyte retrieval,  pregnant

label_protocol: Labeled with biotin using the IVT labeling kit (Affymetrix)

extract_protocol: RNA isolation with RNeasy Mini kit (Qiagen) according to manufacturer' s protocol

treatment_protocol: GnRH-antagonist/rec-FSH stimulated IVF cycle

tag: Endometrial dating d2-3, pregnant


title: Iso 10DAP, Fe limited, biological rep 2

description: Gene expression data from iron deficient IsoClark 10DAP

source_name: IsoClark 10 day roots, Fe limited, biological rep 2

value: Fe limited


title: SCARKO-jsd_testis_rep3

description: gene expression data


title: Clark 10DAP, Fe limited, biological rep 1

source_name: Clark 10 day roots, Fe limited, biological rep 1


title: Clark 14DAP, Fe sustained, biological rep 1

source_name: Clark 14 day roots, Fe sufficient, biological rep 1


title: Iso 10DAP, Fe sufficient, biological rep 3

source_name: IsoClark 10 day roots, Fe sufficient, biological rep 3


title: jsd_testis_rep2

description: gene expression data

source_name: testis from jsd mice

value: jsd


title: jsd_testis_rep3

description: gene expression data


title: Iso 10DAP, Fe sufficient, biological rep 1

source_name: IsoClark 10 day roots, Fe sufficient, biological rep 1


title: jsd_testis_rep1

description: gene expression data


title: Iso 10DAP, Fe limited, biological rep 1

source_name: IsoClark 10 day roots, Fe limited, biological rep 1


title: Patient 1, dye reversal

source_name: in vivo

value: Paratyphi A

source_name: in vitro

value: in vitro (LB media)


title: Patient 1, replicate

value: in vivo (blood of bacteremic patient)


title: Patient 1


title: SCARKO-jsd_testis_rep1

description: gene expression data


title: Iso 10DAP, Fe limited, biological rep 3

source_name: IsoClark 10 day roots, Fe limited, biological rep 3


title: Yeast D10 Small cells compared to pooled WT San I cells, biological replicate 1/4.

status: Public on Sep 03 2010

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description:
Yeast D10 Small 01
Biological replicate 1/4.

hyb_protocol: 825 ng of each labeled cRNA (D10 Small and pooled WT San I) were hybridized to the Agilent Yeast Oligo Microarray V2 (4x44) following the instructions from the manufacturer.

scan_protocol: Arrays scanned on an Tecan LS200 scanner; images analyzed using MediaCybernetics Array-Pro Analyzer software.

data_processing: Raw data deposited to BASE (BioArray Software Environment) and normalized using LOWESS plugin (min. M step: 0.043, iterations: 4, window size: 0.33).

organism: Saccharomyces cerevisiae

source_name: D10 Small 01

label_protocol: Labelling was performed with the Agilent Low RNA Input Linear Amplification Kit (LRILAK) as described by the manufacturer. Briefly, 250 ng RNA were reversed transcribed using T7 promoter primer and MMLV-RT. The obtained cDNAs were then transcribed into labeled cRNA with T7 RNA polymerase in the presence of Cy3-CTP (D10 Small) or Cy5-CTP (pooled WT San I).

growth_protocol: Parental San I and D10 Small translocant cells were grown in YPD medium until OD595 ~ 0.4-0.5. The translocant D10 Small cells were grown in presence of 200 mkg/ml kanamycin (ForMedium, UK).

extract_protocol: Total RNAs was isolated using the RNeasy Mini Kit (Qiagen) following manufacturer's instructions. RNA quantity and purity was assessed using Nanodrop.

tag: strain

value: D10 Small

source_name: pooled WT San I

value: WT San I


title: Yeast D10 Small cells compared to pooled WT San I cells, biological replicate 3/4.

description:
Yeast D10 Small 03
Biological replicate 3/4.

source_name: D10 Small 03


title: Yeast D10 Small cells compared to pooled WT San I cells, biological replicate 2/4.

description:
Yeast D10 Small 02
Biological replicate 2/4.

source_name: D10 Small 02


title: S. lycopersicum cv. Micro-Tom vs  S. lycopersicum cv. Micro-Tom E2FB-ox Rep 3

status: Public on Sep 04 2010

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas

description: Biological replicate 3 of 3. Gene expression of E2FB-ox vs Wild Type Micro-Tom

hyb_protocol: The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050 ver 5.7)

scan_protocol: Images from Cy3 and Hyper5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

organism: Solanum lycopersicum

source_name: true leaves and apical meristems from Solanum lycopersicum cv. Micro-Tom

label_protocol: 5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5  and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop

growth_protocol: Solanum lycopersicum cv. Micro-Tom wild type or E2FB overexpressing plants were grown in MS medium plus 2% of sucrose  in a  chamber under 16-hours light/8 hours dark photoperiod at 24 ºC for 14 days. Afterwards, we cut teh shoot apical meristem and teh true leaves and frozen in liquid nitrogen.

extract_protocol: Total RNA was extracted using the TRIzol® Plus RNA and purified throuhg RNA columns. purification Kit (Invitrogen).  The RNA yield and quality were determined by Nanodrop Spectrophotometer at 260 and 280 nm and bioanalyzer analysis. For microarray analysis, total RNAs were processed for use on TOM1 array

treatment_protocol: We compared the gene expression differences between E2FB overexpresing plant vs wild type.

tag: cultivar

value: Micro-Tom wild type

source_name: true leaves and apical meristems from Solanum lycopersicum cv Micro-Tom E2FB-ox (At5g::)

value: Micro-Tom E2FB-ox (At5g::)


title: S. lycopersicum cv. Micro-Tom vs  S. lycopersicum cv. Micro-Tom E2FB-ox Rep 2

description: Biological replicate 2 of 3. Gene expression of E2FB-ox vs Wild Type Micro-Tom


title: Yeast D10 Small cells compared to pooled WT San I cells, biological replicate 4/4.

description:
Yeast D10 Small 04
Biological replicate 4/4.

source_name: D10 Small 04


title: WT vs rim101 mutant gene expression

city: Lynchburg

first: Michael

middle: S

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

description: dye swaps were performed

hyb_protocol: Hybridization was performed at the Duke University Microarray Facility following the Hybridization protocol (http://www.genome.duke.edu/cores/microarray/).

scan_protocol: Slides were scanned at the Duke University Microarray Facility using an Axon Genepix 4000B scanner (http://www.genome.duke.edu/cores/microarray/).

data_processing: Data was analyzed using JMP genomics (SAS institute, Cary NC) and initial background subtraction was performed. We used ANOVA normalization and FDR analysis to calculate differences between treatment effects for pairs of inducing conditions. Genes were considered for further evaluation if they showed log2-transformed fold changes with a p-value < 0.02.

organism: Cryptococcus neoformans

source_name: WT in capsule inducing medium

label_protocol: Labeling was performed at the Duke University Microarray Facility following the Direct Labeling protocol for spotted arrays (http://www.genome.duke.edu/cores/microarray/).

extract_protocol: RNA was prepared using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA) following manufacturer's instructions.

tag: growth medium

value: DMEM

source_name: rim101 in capsule inducing medium


title: S. lycopersicum cv. Micro-Tom vs  S. lycopersicum cv. Micro-Tom E2FB-ox Rep 1

description: Biological replicate 1 of 3. Gene expression of E2FB-ox vs Wild Type Micro-Tom


title: Control sample

city: Gauting, Munich

first: Srinivas

last: Mamidi

state: Bayern

address: Robert Koch Allee 29

department: Clinical Cooperation Group Inflammatory Lung Diseases

country: Germany

institute: Helmholtz Center Munich

description: Gene expression data from untreated BAL cells.

hyb_protocol: According to the standard Affymetrix protocol

data_processing: Data were normalized, and transcript-specific gene expression levels were calculated, using gcrma (Wu et al., J. Comput. Biol., 12, 882-93, 2005; Wu et al., Nat. Biotechnol. 22, 656-8,, 2004) or rma (Bolstad et al., Bioinformatics, 19, 185-93, 2003; Irizarry et al., Nucleic Acids Res., 31, e15, 2003) as implemented in R (R Development Core Team, R foundation for statistical computing, Vienna, 2007) and Bioconductor (Gentleman et al., Genome Biology, 5, R80, 2004). Differentially expressed genes were identified using the permutation-based method of Tusher et al. (Proc. Natl. Acad. Sci. USA, 98, 5116-21, 2001) (sam) as implemented in the "samr" R package, using the median false discovery rate over 100 data permutations as a measure for statistical significance.

source_name: BAL cells from patients with inflammatory lung diseases

growth_protocol: Cells were cultured in RPMI 1640, L-glutamine 2 mM, Penicillin 200 U/ml, Streptomycin 200µg/m, nonessential amino acids, OPI-supplement and 10% FCS medium for 3 days

extract_protocol: Total RNA was extraction by using TRI reagent according to the manufacturer's instructions.

treatment_protocol: BAL cells cultivated either in the presence of liposomal ATRA (5µM) or left untreated for 3 days.

tag: tissue

value: Lung

tag: agent

value: untreated

value: Adults


title: Liposomal ATRA treated sample

description: Gene expression data from LipATRA treated BAL cells.

scan_protocol: According to the standard Affymetrix protocol

value: liposomal ATRA (5µM)


title: clinical sample 198130

type: genomic

city: New York

first: Rita

last: Shaknovich

state: NY

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medical Center

description: Sample name: 07-30628

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Raw data (.pair) files generated using NimbleScan software. After QC processing, a median normalization was performed on each array by subtracting the median log-ratio (HpaII/MspI) of that array (resulting in median log-ratio of 0 for each array). SignalMap Version 1.9 software used to generate normalized, log2 ratios.  Log2 ratios that were below 2.5MADs of the random probes for each individual array, were considered failed probes and were removed.

molecule: genomic DNA

source_name: DLBCL, MspI representation of genomic DNA

label_protocol: Random priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

value: GCB

tag: pathology

value: DLBC

tag: site

value: LN (Lymph Node)

tag: sex

value: M

tag: txprimary

tag: status

value: Free of disease after initial treatment

value: ALIVE

tag: overall_survival  (years)

tag: progression_free_survival  (years)

source_name: DLBCL, HpaII representation of genomic DNA

tag: overall_survival (years)

tag: progression_free_survival (years)


title: clinical sample 198121

description: Sample name: 07-28351

value: ABC


title: clinical sample 149435

description: Sample name: 06-31353


title: clinical sample 227460

description: Sample name: 07-32561

value: COMPOSITE (>50% DLBCL, remaining FL)


title: clinical sample 146863

description: Sample name: 04-14093

value: F

value: DEAD


title: clinical sample 227461

description: Sample name: 07-30109


title: clinical sample 227526

description: Sample name: 07-23804


title: WT vs gcn5 mutant gene expression under capsule inducing conditions

description: dye swap experiments were performed

hyb_protocol: RNA hybridization was performed by the Duke University Microarray Core Facility according to their established protocols for custom spotted arrays (http://www.genome.duke.edu/cores/microarray/).

data_processing: Data were analyzed using JMP genomics v. 4.1 (SAS Institute, Cary, NC), and initial background subtraction was performed. We used analysis of variance (ANOVA) normalization and false discovery rate (FDR) analysis to calculate differences between treatment effects for pairs of inducing conditions. Genes were considered for further evaluation if they had log2-transformed fold changes greater than 2-fold with a P value of < 0.001.

label_protocol: Twenty microliters of 1ug/ul RNA was submitted to the Duke University Microarray Core Facility for labeling following the Direct Labeling protocol for spotted arrays (http://www.genome.duke.edu/cores/microarray/).

extract_protocol: RNA was prepared from lyophilized samples using the RNeasy kit (Qiagen, Valencia, CA).

source_name: gcn5 in capsule inducing medium


title: clinical sample 149413

description: Sample name: 06-30145

value: With disease, after initial treatment


title: clinical sample 178307

description: Sample name: 06-28900


title: clinical sample 176549

description: Sample name: 06-23792


title: clinical sample 149365

description: Sample name: 06-24718

value: ENT


title: clinical sample 177615

description: Sample name: 06-16716


title: clinical sample 227528

description: Sample name: 95-32814


title: clinical sample 227453

description: Sample name: 07-17613

value: testis


title: clinical sample 149371

description: Sample name: 06-30025


title: clinical sample 148170

description: Sample name: 06-14634


title: clinical sample 177537

description: Sample name: 06-25470


title: clinical sample 148673

description: Sample name: 06-23907


title: clinical sample 149366

description: Sample name: 06-24915


title: clinical sample 147943

description: Sample name: 06-17315

value: NC (not classifiable)


title: clinical sample 177542

description: Sample name: 06-22057

value: Breast


title: clinical sample 227451

description: Sample name: 82-57570

value: gastric

value: LYMPHOMA DEATH


title: KO-021

city: Essen

first: Cyrus

last: Khandanpour

address: Hufelandstr. 55

department: Hematology

institute: University Hospital Essen

description: Gfi1b KO

hyb_protocol: Samples were hybridized with [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Arrays and scanned using a GeneArray Scanner at the Génome Québec INNOVATION centre of the McGill University, Montréal, QC, Canada

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data was processed using the Affymetrix Expression Console software. algorithm-name: rma-gene-default

source_name: 150 pos, CD 48 neg, Lin neg Sca and c-kit pos BM cells

label_protocol: Target RNA was reverse transcribed into cDNA using a NuGEN Ovation Pico RNA Kit and in-vitro transcription was performed to generate biotin-labeled cRNA. cRNA was labeled with streptavidin-phycoerythrin.

extract_protocol: Qiagen micro-RNA kit was used

treatment_protocol: Gfi1bfl/fl and MxCretg gfi1bfl/fl mice were injected 5 times with 500 µg pIpC every other day for a total of 5 injections.

tag: genotype/variation

value: Gfi1b KO


title: clinical sample 124790

description: Sample name: 03-33266

value: GCB

value: DLBC

tag: age


title: clinical sample 126481

description: Sample name: 04-29264

value: LN (Lymph Node)

value: M


title: clinical sample 149297

description: Sample name: 06-16316

value: GI

value: Free of disease after initial treatment

value: ALIVE


title: clinical sample 126490

description: Sample name: 04-14066

value: spleen

value: Free of disease after treatment for first relapse


title: KO-517

description: Gfi1b KO


title: KO-992

description: Gfi1b KO


title: WT-470

description: Gfi1b wt

value: Gfi1b wt


title: clinical sample 124801

description: Sample name: 03-34768


title: clinical sample 126485

description: Sample name: 05-21634

value: ABC

value: DEAD


title: clinical sample 126164

description: Sample name: 04-29995

value: F

value: TOXIC DEATH


title: clinical sample 125131

description: Sample name: 03-31713

value: CHOP-RITU-ABVD


title: Mouse 158, gastrocnemius muscle, high fat diet, week 8

city: Maastricht

first: Janneke

last: de Wilde

address: Universiteitssingel 50

department: Human Biology

country: Netherlands

institute: Maastricht University

description: Before the diet intervention mice (age: 9 weeks) were switched to the LF run-in diet for 3 weeks

hyb_protocol: Hybridization was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)

scan_protocol: Scanning was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)

data_processing:
Expression levels of probe sets were normalized using GC-RMA(slow) (unlogged scale). Probe sets were redefined according to Dai et al (Nucleic Acids Research, 2005). In this method probes are annotated
using up to date databases and assigned to unique gene identifiers, in this case Entrez ID's, instead of the classic GeneChip probe sets. As selection criteria we used: fold change > 1.3  and FDR < 0.05

source_name: mouse 158, gastrocnemius muscle, high fat diet, week 8

label_protocol: Labeling was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)

growth_protocol: Mice were fed a standard growth diet for 3 weeks prior to switching to the LF run-in diet for 3 weeks. Following the run-in period mice randomly assigned to the LF or the HF group for 8 weeks

extract_protocol:
According the manufactures instruction, total RNA was extracted from the quadriceps muscle with Trizol reagent (Invitrogen, Breda, the Netherlands) and purified with the Rneasy Mini Kit
(Qiagen, Venlo, the Netherlands). Contaminating genomic DNA was removed with the RNase-free DNase set (Qiagen, Venlo, the Netherlands) according the manufactures instructions.

treatment_protocol: After 8 weeks of diet intervention, mice were sacrificed, the gastrocnemius and quadriceps muscles were dissected and snap-frozen in liquid nitrogen

tag: subject

value: mouse 158

value: gastrocnemius muscle

tag: diet

value: high fat diet

tag: gender

value: Male

value: 20 weeks


title: Mouse 157, gastrocnemius muscle, high fat diet, week 8

source_name: mouse 157, gastrocnemius muscle, high fat diet, week 8

value: mouse 157

tag: strain


title: Mouse 151, gastrocnemius muscle, high fat diet, week 8

source_name: mouse 151, gastrocnemius muscle, high fat diet, week 8

value: mouse 151

tag: tissue


title: clinical sample 130121

description: Sample name: 05-24561

value: GCB

value: DLBC

value: LN (Lymph Node)

value: M

value: Free of disease after initial treatment


title: WT-628

description: Gfi1b wt

value: Gfi1b wt


title: clinical sample 125130

description: Sample name: 04-11156

value: ALIVE


title: clinical sample 125068

description: Sample name: 04-39108

value: ABC


title: clinical sample 227457

description: Sample name: 07-14026

value: COMPOSITE (>50% DLBCL, remaining FL)


title: Mouse 150, gastrocnemius muscle, high fat diet, week 8

source_name: mouse 150, gastrocnemius muscle, high fat diet, week 8

value: mouse 150


title: WT-080

description: Gfi1b wt


title: Mouse 152, gastrocnemius muscle, high fat diet, week 8

source_name: mouse 152, gastrocnemius muscle, high fat diet, week 8

value: mouse 152


title: Mouse 149, gastrocnemius muscle, high fat diet, week 8

source_name: mouse 149, gastrocnemius muscle, high fat diet, week 8

value: mouse 149

value: gastrocnemius muscle


title: clinical sample 179880

description: Sample name: 06-27347

value: CHOP-RITU


title: clinical sample 125126

description: Sample name: 05-28122

value: LYMPHOMA DEATH

value: DEAD


title: Mouse 146, gastrocnemius muscle, high fat diet, week 8

source_name: mouse 146, gastrocnemius muscle, high fat diet, week 8

value: mouse 146

value: high fat diet

value: Male

value: 20 weeks


title: clinical sample 125125

description: Sample name: 94-26795

value: GCB

value: DLBC

value: LN (Lymph Node)

value: M


title: Mouse 143, gastrocnemius muscle, high fat diet, week 8

source_name: mouse 143, gastrocnemius muscle, high fat diet, week 8

value: mouse 143


title: Mouse 145, gastrocnemius muscle, high fat diet, week 8

source_name: mouse 145, gastrocnemius muscle, high fat diet, week 8

value: mouse 145


title: clinical sample 106067

description: Sample name: 05-25439

value: Receiving treatment for first relapse

value: ALIVE


title: Mouse 144, gastrocnemius muscle, high fat diet, week 8

source_name: mouse 144 gastrocnemius muscle, high fat diet, week 8

value: mouse 144


title: clinical sample 113339

description: Sample name: 05-12224

value: F


title: clinical sample 124545

description: Sample name: 06-11535

value: NC (not classifiable)

value: Free of disease after initial treatment


title: clinical sample 124761

description: Sample name: 06-19919


title: Mouse 145, quadriceps muscle, high fat diet, week 8

source_name: mouse 145, quadriceps muscle, high fat diet, week 8

value: quadriceps muscle


title: Mouse 157, quadriceps muscle, high fat diet, week 8

source_name: mouse 157, quadriceps muscle, high fat diet, week 8

value: mouse 157


title: clinical sample 123578

description: Sample name: 96-15389


title: clinical sample 124060

description: Sample name: 06-18547


title: Mouse 151, quadriceps muscle, high fat diet, week 8

source_name: mouse 151, quadriceps muscle, high fat diet, week 8

value: mouse 151

value: high fat diet


title: Mouse 149, quadriceps muscle, high fat diet, week 8

source_name: mouse 149, quadriceps muscle, high fat diet, week 8

value: mouse 149

value: Male

value: 20 weeks


title: clinical sample 114625

description: Sample name: 05-32947

source_name: DLBCL, MspI representation of genomic DNA

value: GCB

value: DLBC

value: GI

source_name: DLBCL, HpaII representation of genomic DNA


title: clinical sample 125128

description: Sample name: 02-30647

value: LN (Lymph Node)

value: M


title: Root wt CLE10 rep3

city: Kobe

first: Yuki

last: Kondo

address: 1-1 Rokkodai-cho, Nada-ku

department: Graduate School of Science

country: Japan

institute: Kobe University

description: Arabidopsis WT CLE10 12h

hyb_protocol: Hybridization, washing, staining procedures were conducted with Fluidics Station 450 as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

scan_protocol: Scanning procedure ws conducted with GeneChip Scanner 3000 7G as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

data_processing: GCOS 1.4

organism: Arabidopsis thaliana

source_name: Col-0, 7-day-old roots, 5mm root tips

label_protocol: Biotinylated cRNA was prepared from total RNA with GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix).

growth_protocol: Seeds were sterilised with sodium hypochlorite 5 min, 4 rinses sterile water, cultured on MS liquid medium, and incubated at 23ºC under the continuous light conditions with shaking for 7 days.

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) and purified with Rneasy Micro Kit (QIAGEN).

treatment_protocol: Before sampling, roots were treated with chemically synthesized CLE peptide at 1000 nM for 12 hours.

value: root tip


title: Mouse 146, quadriceps muscle, high fat diet, week 8

source_name: mouse 146, quadriceps muscle, high fat diet, week 8

value: mouse 146


title: clinical sample 113362

description: Sample name: 03-16394

value: spleen

value: LYMPHOMA DEATH

value: DEAD


title: Root wt CLE10 rep1

description: Arabidopsis WT CLE10 12h


title: Mouse 158, quadriceps muscle, high fat diet, week 8

source_name: mouse 158, quadriceps muscle, high fat diet, week 8

value: mouse 158

value: quadriceps muscle


title: clinical sample 124573

description: Sample name: 05-12939

value: NC (not classifiable)

value: Free of disease after initial treatment

value: ALIVE


title: clinical sample 125408

description: Sample name: 05-24395


title: Mouse 152, quadriceps muscle, high fat diet, week 8

source_name: mouse 152, quadriceps muscle, high fat diet, week 8

value: mouse 152

value: high fat diet

value: Male


title: clinical sample 113348

description: Sample name: 02-30519

value: DLBC

value: tonsil


title: E18TaBS3

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 12 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: RNAs were isolated by Trizol by standard protocol (Invitorogen). RNA samples were then subjected to LiCl precipitation to eliminate genomic DNA contamination.

tag: cell type

value: Backskin

value: male

tag: development stage

value: embryo

tag: genetic modification

value: Transgenic and Knock down

tag: individual identifier

source_name: Universal Mouse Reference Cell Line Pool

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

value: Universale Mouse Reference


title: Mouse 144, quadriceps muscle, high fat diet, week 8

source_name: mouse 144, quadriceps muscle, high fat diet, week 8

value: mouse 144

value: 20 weeks


title: clinical sample 123576

description: Sample name: 03-13123

value: GCB

tag: pathology

tag: site

value: GI

tag: sex

value: M

tag: txprimary


title: clinical sample 114632

description: Sample name: 06-10398

value: ABC

value: ENT

tag: status

value: Free of disease after treatment for first relapse

value: DEAD

tag: overall_survival  (years)

tag: progression_free_survival  (years)

tag: overall_survival (years)


title: clinical sample 106086

description: Sample name: 05-24666

value: LN (Lymph Node)

tag: age

value: lymphoma DEATH

tag: progression_free_survival (years)


title: Root wt CLE10 rep2

description: Arabidopsis WT CLE10 12h

value: root tip


title: clinical sample 113343

description: Sample name: 04-36183

value: NC (not classifiable)

value: COMPOSITE (>50% DLBCL, remaining FL)

value: LYMPHOMA DEATH


title: clinical sample 128338

description: Sample name: 01-19969

value: DLBC

value: F

value: Free of disease after initial treatment

value: ALIVE


title: Mouse 160, gastrocnemius muscle, low fat diet, week 8

source_name: mouse 160, gastrocnemius muscle, low fat diet, week 8

tag: subject

value: mouse 160

value: gastrocnemius muscle

tag: diet

value: low fat diet

tag: gender

value: Male

value: 20 weeks


title: Mouse 155, gastrocnemius muscle, low fat diet, week 8

source_name: mouse 155, gastrocnemius muscle, low fat diet, week 8

value: mouse 155

tag: tissue

tag: strain


title: clinical sample 125165

description: Sample name: 04-23426

value: spleen

value: M

value: SPLE-CHOP-RITU-RAD


title: clinical sample 143342

description: Sample name: 02-20170

value: ABC

value: LN (Lymph Node)


title: Mouse 150, quadriceps muscle, high fat diet, week 8

source_name: mouse 150, quadriceps muscle, high fat diet, week 8

value: mouse 150

value: quadriceps muscle

value: high fat diet


title: Mouse 156, gastrocnemius muscle, low fat diet, week 8

source_name: mouse 156, gastrocnemius muscle, low fat diet, week 8

value: mouse 156


title: Root wt CLE25 rep3

description: Arabidopsis WT CLE25 12h

value: root tip


title: clinical sample 124574

description: Sample name: 05-24904

value: GCB

value: DLBC

value: thyroid

value: F

value: Free of disease after initial treatment

value: ALIVE


title: clinical sample 128336

description: Sample name: 01-29174


title: E18TaDk4TGBS3

tag: cell type

value: Backskin

value: male

tag: development stage

value: embryo

tag: genetic modification

value: Transgenic and Knock down

value: Universale Mouse Reference


title: Mouse 159, gastrocnemius muscle, low fat diet, week 8

source_name: mouse 159, gastrocnemius muscle, low fat diet, week 8

value: mouse 159

value: gastrocnemius muscle

value: low fat diet

value: Male

value: 20 weeks


title: clinical sample 125320

description: Sample name: 98-22532

tag: pathology

tag: site

value: LN (Lymph Node)

value: M


title: clinical sample 125327

description: Sample name: 05-18695

value: ABC

value: DLBC

tag: sex

tag: txprimary

value: LYMPHOMA DEATH

value: DEAD


title: Root wt CLE25 rep1

description: Arabidopsis WT CLE25 12h

value: root tip


title: Mouse 143, quadriceps muscle, high fat diet, week 8

source_name: mouse 143, quadriceps muscle, high fat diet, week 8

value: mouse 143

value: quadriceps muscle

value: high fat diet


title: clinical sample 124424

description: Sample name: 99-25549

value: F

value: CHOP-RITU

tag: status

tag: overall_survival  (years)


title: clinical sample 145918

description: Sample name: 97-14402

tag: progression_free_survival  (years)

tag: overall_survival (years)


title: clinical sample 130122

description: Sample name: 01-26579

value: GCB

tag: age

value: Free of disease after initial treatment

value: ALIVE

tag: progression_free_survival (years)


title: E18TaBS2

value: Backskin

value: male

value: embryo

value: Transgenic and Knock down

tag: individual identifier

value: Universale Mouse Reference


title: clinical sample 114982

description: Sample name: 03-20981

value: DLBC

value: LN (Lymph Node)

value: DEATH UNRELATED


title: Mouse 154, gastrocnemius muscle, low fat diet, week 8

source_name: mouse 154, gastrocnemius muscle, low fat diet, week 8

tag: subject

value: mouse 154

value: gastrocnemius muscle

tag: diet

value: low fat diet

tag: gender

value: Male

value: 20 weeks


title: clinical sample 108701

description: Sample name: 00-12223

value: M


title: Mouse 153, gastrocnemius muscle, low fat diet, week 8

source_name: mouse 153, gastrocnemius muscle, low fat diet, week 8

value: mouse 153

tag: tissue

tag: strain


title: Root wt CLE25 rep2

description: Arabidopsis WT CLE25 12h

value: root tip


title: clinical sample 178421

description: Sample name: 05-24065

value: ABC

value: Free of disease after initial treatment

value: ALIVE


title: clinical sample 123586

description: Sample name: 05-17793

value: GCB

value: LYMPHOMA DEATH

value: DEAD


title: Mouse 141, gastrocnemius muscle, low fat diet, week 8

source_name: mouse 141, gastrocnemius muscle, low fat diet, week 8

value: mouse 141


title: Mouse 142, gastrocnemius muscle, low fat diet, week 8

source_name: mouse 142, gastrocnemius muscle, low fat diet, week 8

value: mouse 142


title: Mouse 148, gastrocnemius muscle, low fat diet, week 8

source_name: mouse 148, gastrocnemius muscle, low fat diet, week 8

value: mouse 148


title: clinical sample 124254

description: Sample name: 00-26427

source_name: DLBCL, MspI representation of genomic DNA

value: DLBC

value: LN (Lymph Node)

value: Free of disease after treatment for first relapse

source_name: DLBCL, HpaII representation of genomic DNA


title: Mouse 147, gastrocnemius muscle, low fat diet, week 8

source_name: mouse 147, gastrocnemius muscle, low fat diet, week 8

value: mouse 147

value: gastrocnemius muscle

value: low fat diet

value: Male


title: E17TaDk4TGBS2

tag: cell type

value: Backskin

value: male

tag: development stage

value: embryo

tag: genetic modification

value: Transgenic and Knock down

value: Universale Mouse Reference


title: E17TaDk4TGBS3


title: E17TaBS1


title: Mouse 160, quadriceps muscle, low fat diet, week 8

source_name: mouse 160, quadriceps muscle, low fat diet, week 8

value: mouse 160

value: quadriceps muscle

value: 20 weeks


title: E18TaDk4TGBS1

source_name: Universal Mouse Reference Cell Line Pool


title: Tarsal conjunctiva, GAR_221

city: London

first: Martin

middle: James

last: Holland

address: Keppel Street

department: Infectious and Tropical Diseases

country: United Kingdom

institute: London School of Hygiene and Tropical Medicine

hyb_protocol: 15 µg of biotinylated and fragmented cRNA was hybridized to GeneChips (U133 plus 2.0 arrays) for 16 h at 45oC according to the manufacturer’s standard protocols. GeneChips were washed and stained following the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix confocal laser scanner 3000.

data_processing: Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using the RMA package within R BioConductor.

label: Biotin

source_name: Swab, tarsal conjunctiva, N

label_protocol: 100 ng total RNA isolated from an upper tarsal conjunctival swab was subjected to two-rounds of in vitro transcription with biotin-labelled nucleotides (two-cycle cDNA synthesis and labelling kit, Affymetrix, Santa Clara, CA, USA).

extract_protocol: Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Mini-kit (Qiagen Ltd, Crawley, UK).

treatment_protocol: Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc)

value: Tarsal conjunctiva

tag: ethnicity

value: Bambara

tag: fpc trachoma score

tag: equivalent who simplified trachoma score

tag: roche ct/ng pcr amplicor value

value: NEG

tag: ompa copies per swab

tag: disease

value: normal


title: E17TaDk4TGBS1

tag: age


title: E18TaBS1


title: Tarsal conjunctiva, GAR_217

value: Female


title: E18TaDk4TGBS2


title: Tarsal conjunctiva, GAR_220


title: clinical sample 105788

description: Sample name: 02-22991

value: ABC

tag: pathology

value: DLBC

tag: site

value: LN (Lymph Node)

tag: sex

value: F

tag: txprimary

tag: status

value: Free of disease after initial treatment

value: ALIVE

tag: overall_survival  (years)

tag: progression_free_survival  (years)

tag: overall_survival (years)

tag: progression_free_survival (years)


title: E17TaBS2

tag: cell type

value: Backskin

tag: strain

tag: gender

value: male

tag: development stage

value: embryo

tag: genetic modification

tag: individual identifier


title: Mouse 159, quadriceps muscle, low fat diet, week 8

source_name: mouse 159, quadriceps muscle, low fat diet, week 8

tag: subject

value: mouse 159

tag: tissue

tag: diet

value: low fat diet

value: Male


title: Tarsal conjunctiva, GAR_219

value: Tarsal conjunctiva

tag: age

tag: ethnicity

tag: fpc trachoma score

tag: equivalent who simplified trachoma score

tag: roche ct/ng pcr amplicor value

tag: ompa copies per swab

tag: disease


title: Tarsal conjunctiva, GAR_216

value: Bambara


title: Mouse 156, quadriceps muscle, low fat diet, week 8

source_name: mouse 156, quadriceps muscle, low fat diet, week 8

value: mouse 156

value: quadriceps muscle

value: 20 weeks


title: E17TaBS3

value: Transgenic and Knock down

value: Universale Mouse Reference


title: Mouse 155, quadriceps muscle, low fat diet, week 8

source_name: mouse 155, quadriceps muscle, low fat diet, week 8

value: mouse 155


title: Panc-1 TGFβ Treated 1 48 hr

city: grand rapids

first: brian

last: haab

state: MI

address: 333 bostwick avenue NE

department: lab of cancer immunodiagnostics

institute: van andel institute

description: Gene expression data from transforming growth factor beta treated Panc-1 pancreatic cancer cell lines after 48 hours

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Ann Arbor quantile-normalized trimmed-mean method (PMID: 15705192).

source_name: Panc-1 Pancreatic Cancer Cells

label_protocol: Biotinylated cRNA was prepare from 3-5 ug total RNA using standard Affymetrix protocol

growth_protocol: Panc-1 cells were maintained in RPMI-1640 medium with glutamine, supplemented with 10% FBS, penicillin, and streptomycin and tested for mycoplasma contamination. All tissue culture media and media supplements were purchased from Life Technologies (Gaithersburg, MD).

extract_protocol: Total RNA was isolated from the harvested cells using Trizol (Invitrogen) and cleanup performed with an RNeasy kit (Qiagen)

treatment_protocol: Cells were serum-starved for 24 h and then treated with 5 ng/mL porcine transforming growth factor beta 1 (TGF-beta, R&D Systems, Minneapolis, MN) for 48 hours.

value: Pancreas

tag: cell line

tag: treatment group

value: TGFβ Treated 48 hr


title: Mouse 154, quadriceps muscle, low fat diet, week 8

source_name: mouse 154, quadriceps muscle, low fat diet, week 8

value: mouse 154

tag: strain


title: Panc-1 TGFβ Treated 2 48 hr


title: Tarsal conjunctiva, GAR_212

tag: gender

value: NEG

value: normal


title: Tarsal conjunctiva, GAR_218

value: Wolof


title: Tarsal conjunctiva, GAR_215


title: Mouse 153, quadriceps muscle, low fat diet, week 8

source_name: mouse 153, quadriceps muscle, low fat diet, week 8

value: mouse 153


title: Panc-1 Untreated Control 1

description: Gene expression data from untreated Panc-1 pancreatic cancer cell lines

value: Untreated Control


title: Tarsal conjunctiva, GAR_213

value: Male


title: Panc-1 Untreated Control 3


title: Panc-1 TGFβ Treated 3 48 hr


title: Mouse 148, quadriceps muscle, low fat diet, week 8

source_name: mouse 148, quadriceps muscle, low fat diet, week 8

value: mouse 148

value: low fat diet


title: Tarsal conjunctiva, GAR_214

value: Tarsal conjunctiva

value: Female


title: Panc-1 Untreated Control 2


title: Mouse 147, quadriceps muscle, low fat diet, week 8

source_name: mouse 147, quadriceps muscle, low fat diet, week 8

value: mouse 147

value: quadriceps muscle

value: 20 weeks


title: Tarsal conjunctiva, GAR_210

value: Bambara


title: P1DkWT35

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 24 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

tag: cell type

value: Backskin

value: male

value: Transgenic and Knock down

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

value: Universale Mouse Reference


title: Tarsal conjunctiva, GAR_208

value: NEG

value: normal


title: Mouse 142, quadriceps muscle, low fat diet, week 8

source_name: mouse 142, quadriceps muscle, low fat diet, week 8

value: mouse 142


title: P1DkTG33

tag: genetic modification


title: Tarsal conjunctiva, GAR_209


title: P1DkTG31

tag: individual identifier


title: Tarsal conjunctiva, GAR_207


title: Tarsal conjunctiva, GAR_200

source_name: Swab, tarsal conjunctiva, TF

value: Wolof

value: TF

value: trachoma


title: Tarsal conjunctiva, GAR_78

hyb_protocol: Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.

data_processing: Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.

label_protocol: cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).

extract_protocol: Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).

treatment_protocol: Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).

value: tarsal conjunctiva

value: Male

tag: age (years)

value: Fula

tag: equivalent who simplified trachoma grade

tag: roche ct/ng amplicor pcr value


title: P1DkTG29

tag: age


title: Mouse 141, quadriceps muscle, low fat diet, week 8

source_name: mouse 141, quadriceps muscle, low fat diet, week 8

tag: subject

value: mouse 141

tag: tissue

tag: diet

value: low fat diet


title: Tarsal conjunctiva, GAR_211

value: Tarsal conjunctiva

tag: ethnicity

tag: fpc trachoma score

tag: equivalent who simplified trachoma score

tag: roche ct/ng pcr amplicor value


title: Tarsal conjunctiva, GAR_197

tag: ompa copies per swab

tag: disease


title: Tarsal conjunctiva, GAR_74

tag: gender

value: Female


title: Tarsal conjunctiva, GAR_198


title: P1DkWT30

tag: cell type

value: Backskin

tag: strain


title: Tarsal conjunctiva, GAR_206

value: Bambara


title: E18.5DkWT16

value: male

tag: development stage

value: embryo

tag: genetic modification

value: Transgenic and Knock down

tag: individual identifier


title: Tarsal conjunctiva, GAR_204

value: NEG

value: normal


title: P1DkWT34

value: Universale Mouse Reference


title: Tarsal conjunctiva, GAR_57

tag: age (years)

value: Wolof

tag: equivalent who simplified trachoma grade

tag: roche ct/ng amplicor pcr value


title: Tarsal conjunctiva, GAR_205

tag: tissue

tag: age


title: Tarsal conjunctiva, GAR_203

tag: ethnicity


title: Tarsal conjunctiva, GAR_202

tag: fpc trachoma score


title: Tarsal conjunctiva, GAR_176

tag: equivalent who simplified trachoma score

value: TF

value: trachoma


title: Tarsal conjunctiva, GAR_179

tag: roche ct/ng pcr amplicor value


title: Tarsal conjunctiva, GAR_73A

value: tarsal conjunctiva

value: POS

tag: ompa copies per swab


title: Tarsal conjunctiva, GAR_55

value: Male

tag: disease


title: Tarsal conjunctiva, GAR_189

tag: gender


title: E16.5DkTG11

tag: cell type


title: E18.5DkTG18

tag: strain


title: Tarsal conjunctiva, GAR_175


title: E18.5DkTG17

tag: development stage


title: E18.5DkTG15

tag: genetic modification


title: Tarsal conjunctiva, GAR_190


title: E16.5DkTG8

tag: individual identifier


title: E16.5DkTG9


title: Tarsal conjunctiva, GAR_192


title: E14.5DkTG4


title: Tarsal conjunctiva, GAR_164


title: E16.5DkWT1012


title: Tarsal conjunctiva, GAR_174


title: E16.5DkWT10


title: Tarsal conjunctiva, GAR_137


title: Tarsal conjunctiva, GAR_169


title: E16.5DkWT12


title: Tarsal conjunctiva, GAR_148


title: Tarsal conjunctiva, GAR_134


title: Tarsal conjunctiva, GAR_173


title: E18.5DkWT14


title: E14.5DkTG2


title: Tarsal conjunctiva, GAR_147


title: E14.5DkWT6


title: Tarsal conjunctiva, GAR_155


title: Tarsal conjunctiva, GAR_51

source_name: Swab, tarsal conjunctiva, TF/TI

tag: age (years)

value: TF/TI


title: Tarsal conjunctiva, GAR_37

value: Manjago

tag: equivalent who simplified trachoma grade


title: Tarsal conjunctiva, GAR_38

value: Female

tag: roche ct/ng amplicor pcr value


title: Tarsal conjunctiva, GAR_123

tag: tissue

value: Tarsal conjunctiva


title: Tarsal conjunctiva, GAR_35


title: E14.5DkWT1

value: Backskin

tag: age


title: Tarsal conjunctiva, GAR_133

tag: ethnicity


title: E14.5DkTG3

value: male


title: Tarsal conjunctiva, GAR_33

tag: fpc trachoma score


title: Tarsal conjunctiva, GAR_44


title: Tarsal conjunctiva, GAR_132

tag: equivalent who simplified trachoma score


title: Tarsal conjunctiva, GAR_34


title: E18.5DkWT13

value: embryo


title: Tarsal conjunctiva, GAR_29


title: Tarsal conjunctiva, GAR_128

tag: roche ct/ng pcr amplicor value


title: Tarsal conjunctiva, GAR_31

tag: ompa copies per swab


title: Tarsal conjunctiva, GAR_30

value: Serer

tag: disease


title: Tarsal conjunctiva, GAR_124

tag: gender


title: Tarsal conjunctiva, GAR_120


title: Tarsal conjunctiva, GAR_125


title: E14.5DkWT5

tag: cell type

value: Transgenic and Knock down


title: Tarsal conjunctiva, GAR_118

value: NEG


title: Tarsal conjunctiva, GAR_25

value: normal


title: Tarsal conjunctiva, GAR_26


title: Tarsal conjunctiva, GAR_27


title: Tarsal conjunctiva, GAR_119

value: Wolof


title: WT TS, biological repeat2

first: Morito

last: Sakaue

state: Hyogo

address: 2-2-3 Minatojimaminamimachi, Chuoku

department: CDB

institute: RIKEN

description: Gene expression data from trophoblastic stem cells derived from a wild-type blastocyst

hyb_protocol: Labeled cRNAs were fragmented and hybridized to Affymetrix GeneChip arrays according to the manufacturer’s instructions. GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: Probe set signal intensities of the CHP files were calculated using MAS5.0.

source_name: mouse wild-type (WT) TS

label_protocol: Double-stranded cDNAs synthesized from the RNA samples were subjected to the one-cycle target labeling procedure for biotin labeling by in vitro transcription (Affymetrix).

growth_protocol: The TS cells were maintained in RPMI 1640 GlutaMax (Invitrogen) supplemented with 20% fetal bovine serum, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 25 ng/ml FGF4, and 1 micro-g/ml heparin with mouse embryonic fibroblast feeder cells.

extract_protocol: Total RNA samples were extracted from the cells using Trizol Reagent (Invitrogen) and cleaned up using an RN-easy column (Qiagen) according to these manufacturers' instructions.

treatment_protocol: The TS cells from a 12.5-cm2 flask at 70-80% confluency were plated on a 75-cm2 flask with feeder cells (mouse embryonic fibroblasts), and cultured for three days. The medium was replaced with fresh medium on the second day. To remove feeder cells from the TS cell culture, the trypsinized cell suspension in the medium was plated on a culture dish and incubated at 37˚C, 5% CO2 for 30 minutes. The supernatant of the cell suspension was collected and used for RNA preparation.

tag: cell line

value: Line 5

tag: genotype

value: Wild type, carrying the GFP transgene

value: Trophoblastic stem (TS) cells derived from a wild-type blastocyst (BDF1xC57BL/6, TgN(acro/act-EGFP)OsbC3-N01-FJ002)


title: Tarsal conjunctiva, GAR_28

value: tarsal conjunctiva

value: TF

value: POS

value: trachoma


title: Tarsal conjunctiva, GAR_130

value: Male


title: WT XEN, biological repeat1

description: Gene expression data from extraembryonic endoderm (XEN) cells derived from a wild-type blastocyst

hyb_protocol: Labeled cRNAs were fragmented and hybridized to Affymetrix GeneChip arrays according to the manufacturer’s instructions. The GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450.

source_name: mouse wild-type (WT) XEN

growth_protocol: The XEN cells were maintained in RPMI 1640 GlutaMax (Invitrogen) supplemented with 20% fetal bovine serum, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol with mouse embryonic fibroblast feeder cells.

treatment_protocol: The XEN cells from a 12.5-cm2 flask at 70-80% confluency were plated on a 75-cm2 flask with feeder cells (mouse embryonic fibroblasts), and cultured for five days. The medium was replaced with fresh medium on the second and fourth days. The cells were recovered by trypsinization. To remove feeder cells, the XEN cells were purified by sorting with a flowcytometer, using green fluorescence as an indicator, and approximately 1 x 10^6 cells were collected for each purification.

value: Line 1

value: Wild type, carrying GFP transgene

value: Extraembryonic endoderm (XEN) stem cells, derived from a wild-type blastocyst (BDF1xC57BL/6, TgN(acro/act-EGFP)OsbC3-N01-FJ002)


title: Tarsal conjunctiva, GAR_113

value: Tarsal conjunctiva

value: Bambara


title: Tarsal conjunctiva, GAR_112

value: Female


title: Tarsal conjunctiva, GAR_17

value: Manjago

value: NEG


title: Tarsal conjunctiva, GAR_117

value: Wolof


title: TKO ntTS, biological repeat1

description: Gene expression data from trophoblastic stem cells derived from nuclear transferred embryos with a mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cell as the nuclear donor

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ntTS

growth_protocol: The ntTS cells were maintained in RPMI 1640 GlutaMax (Invitrogen) supplemented with 20% fetal bovine serum, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 25 ng/ml FGF4, and 1 micro-g/ml heparin with mouse embryonic fibroblast feeder cells.

treatment_protocol: One-third of the ntTS cells from a 10-cm dish at 70-80% confluency were plated on a 10-cm dish with feeder cells (mouse embryonic fibroblasts), and cultured for one day. To remove feeder cells from the TS cell culture, the trypsinized cell suspension in the medium was plated on a culture dish and incubated at 37˚C, 5% CO2 for 30 minutes. The supernatant of the cell suspension was collected and used for RNA preparation.

value: Dnmt1-/-Dnmt3a-/-Dnmt3b-/-, carrying the CAG-GFP transgene

value: nuclear transfer trophoblastic stem (ntTS) cells, derived from nuclear transferred blastocyst


title: Tarsal conjunctiva, GAR_24

source_name: Swab, tarsal conjunctiva, N

value: normal


title: WT XEN, biological repeat2

value: Line 2


title: WT TS, biological repeat1

value: Wild type, carrying the GFP transgene

value: Trophoblastic stem (TS) cells derived from a wild-type blastocyst (BDF1xC57BL/6, TgN(acro/act-EGFP)OsbC3-N01-FJ002)


title: WT ntTS, biological repeat1

description: Gene expression data from trophoblastic stem cells derived from nuclear transferred embryos with a mouse WT ES cell as the nuclear donor

source_name: mouse wild-type (WT) ntTS

value: Line 9.2

value: Wild type, carrying the CAG-GFP transgene


title: mesenchymal stromal cells (MSCs) sample 1

city: Toronto

first: Freda

last: Miller

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

description: RMA expression value derived from Expression Console software; gene-core analysis

hyb_protocol: Samples were hybridized with GeneChip Rat Gene 1.0 ST Arrays (Affymetrix) and scanned at the HSC Microarray Facility.

data_processing: The data were background corrected and normalized using standard RMA procedure implemented in the Affymetrix Expression Console software. The preprocessed data were analyzed using the LIMMA Bioconductor package to identify genes that show significant evidence of differential expression between SKPs and MSCs.

organism: Rattus norvegicus

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was extracted using Trizol (Invitrogen), as per the manufacturer’s instructions, followed by the RNeasy Mini Kit (Qiagen).

tag: cell passage

value: twiced-passaged cells

tag: strain

value: Sprague Dawley

value: mesenchymal stromal cells (MSCs)


title: Tarsal conjunctiva, GAR_111

value: Tarsal conjunctiva

value: TF

value: trachoma


title: ventral SKPs sample 3

source_name: ventral SKPs sample 3

value: ventral SKPs


title: Tarsal conjunctiva, GAR_20

value: tarsal conjunctiva

value: Male

tag: age (years)

value: Manjago

value: POS


title: mesenchymal stromal cells (MSCs) sample 3


title: facial SKPs sample 2

source_name: facial SKPs sample 2

value: facial SKPs


title: Tarsal conjunctiva, GAR_23

value: Female

tag: equivalent who simplified trachoma grade

value: NEG


title: Tarsal conjunctiva, GAR_12

tag: roche ct/ng amplicor pcr value


title: Tarsal conjunctiva, GAR_14

tag: tissue

value: normal


title: Tarsal conjunctiva, GAR_04


title: TKO ntTS, biological repeat2

value: Line 1

value: Dnmt1-/-Dnmt3a-/-Dnmt3b-/-, carrying the CAG-GFP transgene

value: nuclear transfer trophoblastic stem (ntTS) cells, derived from nuclear transferred blastocyst


title: ventral SKPs sample 2

source_name: ventral SKPs sample 2

value: twiced-passaged cells

value: Sprague Dawley


title: Tarsal conjunctiva, GAR_16


title: facial SKPs sample 3

source_name: facial SKPs sample 3


title: WT ntTS, biological repeat2

value: Line 9.2

value: Wild type, carrying the CAG-GFP transgene


title: Tarsal conjunctiva, GAR_15


title: Tarsal conjunctiva, GAR_108

value: Tarsal conjunctiva

tag: age

value: Wolof

value: TF

value: trachoma


title: Tarsal conjunctiva, GAR_106

value: Male

tag: ethnicity

value: TF/TI


title: WT ES+GATA4, biological repeat2

description: Gene expression data from primitive endoderm cells differentiated from mouse WT ES cells

source_name: mouse wild-type (WT) Gata4GR ES +Dex

growth_protocol: ES cells carrying a transgene encoding Gata4 fused with the ligand-binding domain of human glucocorticoid receptor (Gata4GR) driven by the CAG promoter, which can be activated by the addition of dexamethasone (Dex), were maintained in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 10% fetal bovine serum, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and 2000 U/ml leukemia inhibitory factor on gelatinized culture dishes.

treatment_protocol: ES cells carrying the Gata4GR transgene were plated at 1 x 10^4 cells in a 10-cm gelatinized dish in medium without dexamethasone (Dex). The next day, the medium was replaced with fresh medium containing 100 nM Dex. The total RNA was prepared from these cells after culturing them for more 4 days.

value: Line J1G4.2

value: wild type, carrying the Gata4GR transgene

value: Primitive endoderm cells differentiated from ES cells


title: ventral SKPs sample 1

source_name: ventral SKPs sample 1

value: ventral SKPs


title: Tarsal conjunctiva, GAR_100

tag: fpc trachoma score

value: POS


title: Tarsal conjunctiva, GAR_01

source_name: Swab, tarsal conjunctiva, T0

value: tarsal conjunctiva

value: Manjago

value: NEG

value: normal


title: Tarsal conjunctiva, GAR_102

value: Female

tag: equivalent who simplified trachoma score


title: Tarsal conjunctiva, GAR_103

tag: roche ct/ng pcr amplicor value


title: mesenchymal stromal cells (MSCs) sample 2

value: twiced-passaged cells

value: Sprague Dawley

value: mesenchymal stromal cells (MSCs)


title: facial SKPs sample 1

source_name: facial SKPs sample 1

value: facial SKPs


title: WT ES, biological repeat2

description: Gene expression data from mouse WT ES cells

source_name: mouse wild-type (WT) ES

growth_protocol: The ES cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 10% KNOCKOUT Serum Replacement (Invitrogen), 10 micro-M human adrenocorticotrophic hormone (Kurabo), 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and 2000 U/ml leukemia inhibitory factor, on gelatinized culture dishes without feeder cells.

treatment_protocol: ES cells were plated at 1.25 x10^6 cells in a 10-cm gelatinized dish and cultured for two days. The medium was replaced with fresh medium, and the total RNA was extracted from these cells on the following day.

value: Line J1

value: wild type

value: embryonic stem (ES) cells


title: TKO ES, biological repeat2

description: Gene expression data from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells

source_name: mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES

value: Line 19-1


title: Tarsal conjunctiva, GAR_073B

source_name: Swab, tarsal conjunctiva, TF

value: Tarsal conjunctiva

value: Fula

value: TF

tag: ompa copies per swab

value: trachoma


title: mesenchymal stromal cells (MSCs) sample 4


title: prolactinoma untreated with bromocriptine sample 2

status: Public on Sep 02 2010

city: wenzhou

first: wu

middle: zhe

last: bao

address: west road of xueyuan

department: Department of Neurosurgery

country: China

institute: First Affiliated Hospital of Wenzhou Medical College

description: reference (pool of sample 1-6)

hyb_protocol: Exiqon protocol; The fluorescently labeled samples were combined and hybridized to a miRNA microarray (v.10.0, Exiqon, Denmark), in a nitrogen atmosphere.

scan_protocol: GenePix Pro 6.0.The microarray slides were scanned with GenePix 4000B Scanner.

data_processing: The GPR file was extracted and exported to Genespring 7.3.1. The raw data were normalized using Data transformation: set measurements less than 0.01 to 0.01, per spot and per chip: Intensity dependent (Lowess) normalization, and per gene: normalize to median

label_protocol: miRCURY LNA Array power labeling kit (Exiqon, Denmark)

extract_protocol: Total RNA was extracted from pituitary adenoma tissues using Trizol Reagent (Invitrogen Life Technologies, USA) according to the manufacturer’s instructions with some modifications.

treatment_protocol: three of samples were treated with bromocriptine , no less than 5 mg per day was taken at least 8-week-long.

value: male

value: prolactinoma

tag: treatment

value: untreated

source_name: human prolactinoma

value: pool of all 6 treated and untreated prolactinomas


title: WT ES, biological repeat1

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affimetrix).


title: P. gingivalis ATCC 33277, untreated

city: Rostock

first: Sylvio

last: Redanz

state: Mecklenburg Vorpommern

address: Schillingallee 70

department: Institute of microbiology, virology and hygiene

institute: hospital university rostock

description: This sample is of untreated wild-type Porphyromonas gingivalis ATCC 33277. The RNA was pooled from two independent biological replicates, each from separate cultures.

hyb_protocol: Hybridization was executed as recommended by the array user guide (Gene Expression Analysis v 2.0, NimbleGen).

scan_protocol: Scanning was performed with the DNA Microarray Scanner (Agilent) at a resolution of 5 µm and NimbleScanTM version 2.4 software.

data_processing: The raw data (.pair files) were checked for inhomogenous hybridization. Quantile normalization was performed as implemented by GeneSpring GX 11.0, Agilent Technologies.

organism: Porphyromonas gingivalis ATCC 33277

source_name: Untreated

label_protocol: Labeling with Cy3 was executed as recommended by the array user guide (Gene Expression Analysis v 2.0, NimbleGen).

growth_protocol: P. gingivalis (ATCC 33277) was cultured under anaerobic conditions (Anaerocult, Merck, Darmstadt, Germany) at 37°C in medium comprised of 15 g trypticase peptone, 5 g neutralized soja peptone, 5 g sodium chloride, 5 g yeast extract, 0.5 g L-cysteine per litre, and supplemented with 10 mg vitamin K and 5 mg hemin.

extract_protocol: Harvested cells were resuspended in PBS (100 µl) and mixed with TE-Buffer (500 µl), 1% SDS, phenol and lysing matrix B (0,4 g) (MP Biomedicals, Irvine, USA). Cells were lysed by FastPrep®-24-System (MP Biomedicals, Irvine, USA) (2 × 50 sec, 5.0 m/s2) and RNA-isolation was followed by phenol-chloroform-extraction and ethanol-precipitation. Removal of DNA was performed by NucleoSpin®rDNase (Machery-Nagel, Düren, Germany) according to the manufacturer's instructions.

treatment_protocol: For gene-array analysis, a 4 ml aliquot from a 3 days liquid culture (per 1 L: 15 g trypticase peptone, 5 g neutralized soja peptone, 5 g sodium chloride, 5 g yeast extract, 0.5 g L-cysteine, supplemented with 10 mg vitamin K and 5 mg hemin) was inoculated into fresh medium to render an OD660 0.05 and cultivated for 12 h. Using this culture, 4 ml with an OD660 value of 0.1 were incubated with 100 µg/ml Myrothamnus flabellifolia or medium alone (control group) for 6 h.

value: wildtype

tag: phenotype

value: strong adhesion


title: P. gingivalis ATCC 33277, MF-treated

description: This sample is of MF-treated wild-type Porphyromonas gingivalis ATCC33277. The RNA was pooled from two independent biological replicates, each from separate cultures.

source_name: Treated with MF

value: polyphenol-enriched extract from Myrothamnus flabellifolia

value: reduced adhesion


title: TKO ES, biological repeat1

tag: cell type


title: prolactinoma treated with bromocriptine sample 2

description: reference (pool of sample 1-6)

source_name: prolactinoma treated with bromocriptine

tag: gender

value: bromocriptine


title: prolactinoma treated with bromocriptine sample 3

description: reference (pool of sample 1-6)

value: female


title: prolactinoma untreated with bromocriptine sample 1

description: reference (pool of sample 1-6)


title: prolactinoma treated with bromocriptine sample 1

description: reference (pool of sample 1-6)


title: prolactinoma untreated with bromocriptine sample 3

description: reference (pool of sample 1-6)


title: CO92_Cy5_R5_Cy3

city: Rockville

first: John

last: Braisted

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in hybridization buffer as defined by the Agilent Oligonucleotide Array-Based CGH protocol.  Resuspended probes were denatured at 95 degree Celcius and held at 37 degree Celcius prior to hybridization.  The probe mixture then was added to the Agilent microarray slide and allowed to hybridize for 24 hours rotating at 20 rpm in a hybridization oven at 65 degree Celcius.   Hybridized slides were washed sequentially as defined by the Agilent Oligonucleotide Array-Based CGH protocol.

scan_protocol: Scanned on Axon GenePix 4000 scanner.  PMT values were optimized during scanning to balance channel intensities.

data_processing: log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY from  from default normalized Agilent Feature Extraction settings for 2 channel arrays

organism: Yersinia pestis

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen).  Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).The purified labelled DNA was then dye coupled with the appropriate cye dye (CY3/CY5).

growth_protocol: Cells grown in Lysogeny broth (LB) at 37 degrees Celcius overnight.

extract_protocol: Genomic DNA was isolated by lysozyme and proteinase K treatment.


title: WT ES+GATA4, biological repeat1

tag: cell line

value: Line J1G4.2

tag: genotype

value: wild type, carrying the Gata4GR transgene

value: Primitive endoderm cells differentiated from ES cells


title: Unexpired U133Plus2_B_rep2

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

description: Ambion Human Brain Reference RNA

hyb_protocol: The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the GeneChip® 3’-Amplification Reagent Kit for IVT Labeling (Affymetrix). The A260/A280 ratio and yield of each of the cRNAs were recorded. For each sample, 10 µg of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to a GeneChip® microarray for 16 hours at 45ºC.

scan_protocol: Following hybridization, all microarrays were washed and stained in an Affymetrix GeneChip® Fluidics Station. Stained microarrays were scanned with an Affymetrix GeneChip® Scanner 3000.

data_processing: Quality checks and data analyses were carried out using Affymetrix GeneChip® Operating Software (GCOS) and Quality Reporter.

source_name: MAQC sample B, i.e., Ambion Human Brain Reference RNA (HBRR, Catalog #6050)

label_protocol: Biotinylated cRNA samples were prepared according to the standard Affymetrix GeneChip® protocol. One µg of total RNA from each sample, along with poly A spikes (labeling control), were converted to double-stranded cDNA with GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA). After second-strand synthesis, the cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix).

extract_protocol: The two RNA samples had been stored under  80°C at their respective vendor’ freezer since 2005, and were shipped with dry ice from the vendors to the microarray laboratory of Dr. Charles Wang at UCLA. The same batches of the two samples as those used in the MAQC project in 2005 were used in this study. Upon receiving RNA samples in 2009, the microarray laboratory evaluated and confirmed their quality using the RNA 6000 LabChip and Agilent 2100 Bioanalyzer. The RNA Integrity Number (RIN) for each sample was around 8.0.

value: brain reference


title: Tarsal conjunctiva, GAR_104

value: Tarsal conjunctiva

value: Female

value: Wolof

value: POS

tag: disease


title: CO92_Cy5_IKE_GAKI_Cy3

tag: strain


title: Unexpired U133Plus2_A_rep2

source_name: MAQC sample A, i.e., Stratagene Universal Human Reference RNA (UHRR, Catalog #740000)

value: universal reference


title: Unexpired U133Plus2_A_rep3

description: Stratagene Universal Human Reference RNA


title: CO92_Cy5_YERS020_Cy3


title: CO92_Cy5_MD67_Cy3


title: Unexpired U133Plus2_B_rep1

description: Ambion Human Brain Reference RNA


title: CO92_Cy5_ZE94_Cy3


title: Unexpired U133Plus2_B_rep3

description: Ambion Human Brain Reference RNA


title: CO92_Cy5_YERS061_Cy3


title: CO92_Cy5_PB1_PLUS_Cy3


title: CO92_Cy5_YERS017_Cy3


title: CO92_Cy5_MSU_D_Cy3


title: Unexpired U133Plus2_A_rep1


title: CO92_Cy5_Neilson_Cy3

source_name: Neilson

value: Neilson


title: CO92_Cy5_P13_Cy3


title: CO92_Cy5_1774_Cy3


title: CO92_Cy5_YERS018_Cy3


title: CO92_Cy5_CO96_3188_Cy3


title: CO92_Cy5_H35_Cy3


title: CO92_Cy5_K25_Cy3


title: CO92_Cy5_7_Cy3


title: CO92_Cy5_India_Cy3

source_name: India

value: India


title: CO92_Cy5_16_34_Cy3


title: CO92_Cy5_15_91_Cy3


title: CO92_Cy5_PB1_0_Cy3


title: Tarsal conjunctiva, GAR_101

value: Male

value: TF

value: NEG

value: trachoma


title: CO92_Cy5_1779_Cy3


title: CO92_Cy5_A1122_Cy3


title: CO92_Cy5_D27_Cy3


title: CO92_Cy5_111_65_Cy3


title: CO92_Cy5_MSU_H_Cy3


title: CO92_Cy5_Parkin4_Cy3


title: CO92_Cy5_YERS022_Cy3


title: CO92_Cy5_NUMBER14_Cy3


title: CO92_Cy5_MD31_Cy3


title: CO92_Cy5_32_Cy3


title: CO92_Cy5_CO99_3015_Cy3


title: CO92_Cy5_YERS014_Cy3


title: CO92_Cy5_169_032_Cy3


title: CO92_Cy5_YERS019_Cy3


title: CO92_Cy5_NR15_Cy3


title: CO92_Cy5_YERS023_Cy3


title: CO92_Cy5_CO99_B_3015_Cy3


title: CO92_Cy5_F361_66_Cy3


title: CO92_Cy5_YP13979_Cy3


title: CO92_Cy5_YS06_Cy3


title: CO92_Cy5_PA3606_Cy3


title: CO92_Cy5_YP1851_Cy3


title: CO92_Cy5_195_P_P15_Cy3


title: CO92_Cy5_YP1807AJ_Cy3


title: CO92_Cy5_YP6903_Cy3


title: CO92_Cy5_CO97_5598_Cy3


title: CO92_Cy5_YP3066_Cy3

treatment_protocol: None.


title: CO92_Cy5_YP8906_Cy3


title: CO92_Cy5_YpTB908_Cy3

organism: Yersinia pseudotuberculosis


title: CO92_Cy5_YpTB27802_Cy3


title: CO92_Cy5_KIM6plusD1_Cy3


title: CO92_Cy5_YP8786_Cy3


title: CO92_Cy5_YP8787_Cy3


title: CO92_Cy5_YP8791_Cy3


title: CO92_Cy5_YT01_Cy3


title: CO92_Cy5_YP2095_Cy3


title: CO92_Cy5_KIM6plus_Cy3


title: CO92_Cy5_NR2715_Cy3


title: CO92_Cy5_YPC-14735_Cy3


title: CO92_Cy5_YP_C2944_Cy3


title: CO92_Cy5_YP29833_Cy3


title: CO92_Cy5_YP1412_Cy3


title: CO92_Cy5_P12_Cy3


title: CO92_Cy5_YP3072_Cy3


title: CO92_Cy5_YpTBIP325_Cy3


title: CO92_Cy5_YP909_Cy3


title: CO92_Cy5_YP_C2614_Cy3


title: CO92_Cy5__YP_C1522_Cy3


title: CO92_Cy5_13974_Cy3


title: CO92_Cy5_ATCC23207_Cy3


title: CO92_Cy5_YP8907_Cy3


title: CO92_Cy5_YpTB13980_Cy3


title: CO92_Cy5_YS03_Cy3


title: CO92_Cy5_YP8788_Cy3


title: CO92_Cy5_32[EPI]_Cy3


title: CO92_Cy5_PestoidesG_Cy3

source_name: PestoidesG

value: PestoidesG


title: CO92_Cy5_YP8792_Cy3


title: CO92_Cy5_YP3757_Cy3


title: CO92_Cy5_NR2719_Cy3


title: CO92_Cy5_PestoidesI_Cy3

source_name: PestoidesI

value: PestoidesI


title: CO92_Cy5_YP23207


title: CO92_Cy5_IP32593_Cy3


title: CO92_Cy5_YP3064_Cy3


title: CO92_Cy5_YS02_Cy3


title: CO92_Cy5_NR2718_Cy3


title: CO92_Cy5_YP103AJ_Cy3


title: CO92_Cy5_YP9610_Cy3


title: CO92_Cy5_1954_Cy3


title: CO92_Cy5_YP129-AJ_Cy3


title: CO92_Cy5_YP1391_Cy3


title: CO92_Cy5_PexU2_Cy3


title: CO92_Cy5_YP8793_Cy3


title: CO92_Cy5_YP3065_Cy3


title: CO92_Cy5_YS05_Cy3


title: CO92_Cy5_YP3083_Cy3


title: CO92_Cy5_PB6_Cy3


title: CO92_Cy5_YpTB6905_Cy3


title: CO92_Cy5_YP3768_Cy3


title: CO92_Cy5_YpTB4284_Cy3


title: CO92_Cy5_KIM10_Cy3


title: CO92_Cy5_YP3770_Cy3


title: CO92_Cy5_YpTB6904_Cy3


title: CO92_Cy5_YP3073_Cy3


title: CO92_Cy5_YP8789_Cy3


title: CO92_Cy5_ATCC_ZE-94_Cy3


title: CD8+T_rep1

first: Nicole

last: Suciu-Foca

department: Pathology and Cell Biology

institute: Columbia University

description: Gene expression data from primed human CD8 T cells treated with ILT3Fc

hyb_protocol: Standard hybridization methods provided by Columbia University Core Facilities

scan_protocol: Feature Extraction Software (Version 10.5 Agilent Techology)

data_processing:
Normalization was performed with limmaGUI. Raw intensities were normalized using the within-slides global lowess protocol without background correction.
Differential expression was analzed using Linear Model for MicroArrays (LIMMA).
A cutoff of the Bayesian log-odds of differential expression, B>0, a p value < 0.001 and a Benjamini-Hochberg false discovery rate < 0.1 were used to consider genes for further analysis.

source_name: primed ILT3Fc-treated CD8+ T cells

label_protocol: cDNA obtained from 1 ug total RNA was used directly for synthesis and labeling of cRNA using Quick-Amp Labeling kit and Cyanine CTP 2 color dyes (Agilent Techologies)

growth_protocol: CD3+CD25- T cells were stimulated with allogeneic APC for  7 days in the presence and absence of ILT3Fc; these cells were restimulated with the same APC for 4 hours.

extract_protocol: CD8+ T cells were magnetically sorted out. Total RNA was prepared from cells using the Absolutely RNA extraction kit (Stratagene).

treatment_protocol: ILT3Fc (50 ug/ml) was added to T cells during in the initial priming stage with allogeneic APC; autologous T cells primed with the same APC but without ILT3-Fc were used as controls.

value: CD8+ T cells

value: ILT3Fc(50 ug/ml)

source_name: primed, untreated CD8 T cells

value: untreated


title: CO92_Cy5_YeATCC_Cy3

source_name: YeATCC

value: YeATCC


title: CO92_Cy5_Y228_Cy3


title: CO92_Cy5_YpTB43_Cy3


title: CO92_Cy5_YP1954_Cy3


title: CO92_Cy5_YP1852_Cy3


title: CO92_Cy5_YP1853_Cy3


title: CO92_Cy5_YPC-771_Cy3


title: CO92_Cy5_YP1392_Cy3


title: CD8+T_rep2


title: CD8+T_rep4


title: CO92_Cy5_NEPAL_Cy3

source_name: NEPAL

value: NEPAL


title: CO92_Cy5_HARBIN_Cy3

source_name: HARBIN

value: HARBIN


title: CO92_Cy5_YP1393_Cy3


title: CO92_Cy5_YP1390_Cy3


title: CO92_Cy5_YpTB910_Cy3


title: CD8+T_rep3


title: Macrophages_stimulated_double-KO_1

city: Münster

first: Nils

middle: H

last: Thoennissen

address: Albert-Schweitzer-Str. 33

department: Hematology Oncology

institute: University Hospital of Münster

hyb_protocol: As recommended by the manufacturer (Affymetrix).

scan_protocol: Affymetrix Scanner 3000, as recommended by the manufacturer (Affymetrix).

data_processing: Data were normalized using RMA (Expression Console).

source_name: macrophages, double-KO

extract_protocol: Trizol method (Sigma)

treatment_protocol: The macrophages were stimulated with both LPS (100 ng) and IFN-gamma (100 ng) for 24h.

value: CEBPB/CEBPE double-knockout

value: bone marrow-derived macrophages

value: female

value: 6-8 weeks

value: lipopolysaccharide (LPS) and interferon-gamma (IFN-gamma)


title: CO92_Cy5_PESTOIDES_B_Cy3


title: Macrophages_stimulated_CEBPE-KO_1

source_name: macrophages, CEBPE-KO

label_protocol: As recommended by the manufacturer (Affymetrix).

value: CEBPE-knockout


title: Macrophages_stimulated_CEBPB-KO_1

source_name: macrophages, CEBPB-KO

value: CEBPB-knockout


title: Macrophages_stimulated_WT_1

source_name: macrophages, WT

value: wild-type


title: CO92_Cy5_YP8794_Cy3


title: CO92_Cy5_YP3769_Cy3


title: leaf_10am _day1

city: Johnston

first: Kevin

middle: Robert

last: Hayes

state: IA

address: 7200 NW 62nd Ave

institute: Pioneer Hi-Bred International

description: Gene Expression at leaf_10am_rep1 _day1

hyb_protocol: Standard Agilent Hybridization protocol

scan_protocol: After hybridization, the microarray slides were washed and scanned immediately with Agilent’s G2505B DNA Microarray Scanner at two laser power settings (100% and 10%).  The images were inspected visually for image artifacts, and feature intensities were extracted, filtered, and normalized with Agilent’s Feature Extraction Software (v 9.5.1).

data_processing: The data were then normalized using quantile normalization (BOLSTAD http://www.ncbi.nlm.nih.gov/pubmed/12538238) and passed forward for periodicity determination.  Further quality control and downstream analysis were performed using data analysis tools in Rosetta’s Resolver Database and in the statistical program R

label: Cy3, Cy5

organism: Zea mays

source_name: leaf_10am_rep1 _day1

label_protocol: Each mRNA sample was made into double-stranded DNA, amplified by an in-vitro transcription reaction, and labeled with Cy3 or Cy5 fluorescent dye, all using Agilent’s Low RNA Linear Amp kit.  Biological replicates were labeled alternately using Cy3 or Cy5 to guard against dye-bias.

growth_protocol: Plants of the public inbred line B73 were grown under field conditions in Johnston, Iowa,  U.S.A. to V14-V15 stages, as defined according to the appearance of the leaf collar of the uppermost leaf

extract_protocol: Total RNA was isolated from frozen ground tissue (SQ Tissue Kit, Omega Biotek), followed by polyA RNA isolation (Illustra mRNA Purification Kit, GE Biosciences) for the 108 samples.  The total RNA and polyA RNA samples were visualized and quantified on Agilent’s Bioanalyzer to check for degradation and to determine the concentration.

treatment_protocol: For Agilent microarray profiling, samples were taken starting at daybreak on day 1 (ZT0), and taken every 4 hours hence for 72 hours.  At each time point, the middle section of the top leaf, excluding the midrib, was pooled together with leaves from two separate plants to create one of three biological field replicates.

value: Leaf

tag: cultivar

tag: developmental stage

tag: time

value: 10am  day1


title: leaf_6am _day2

description: Gene Expression at leaf_6am_rep1 _day2

source_name: leaf_6am_rep1 _day2

tag: tissue

value: 6am  day2


title: leaf_6am _day1

description: Gene Expression at leaf_6am_rep1 _day1

source_name: leaf_6am_rep1 _day1

value: 6am  day1


title: CO92_Cy5_YP_CO99_Cy3


title: CO92_Cy5_YP_C1045_Cy3


title: leaf_10am _day2

description: Gene Expression at leaf_10am_rep1 _day2

source_name: leaf_10am_rep1 _day2

value: 10am  day2


title: CO92_Cy5_YPS_D27_Cy3


title: CO92_Cy5_YP3082_Cy3


title: CO92_Cy5_YP3067_Cy3


title: leaf_2pm _day1

description: Gene Expression at leaf_2pm_rep1 _day1

source_name: leaf_2pm_rep1 _day1

value: 2pm  day1


title: leaf_10pm _day1

description: Gene Expression at leaf_10pm_rep1 _day1

source_name: leaf_10pm_rep1 _day1

value: 10pm  day1


title: CO92_Cy5_YPC790_Cy3


title: leaf_6pm _day1

description: Gene Expression at leaf_6pm_rep1 _day1

source_name: leaf_6pm_rep1 _day1

value: 6pm  day1


title: leaf_6pm _day2

description: Gene Expression at leaf_6pm_rep1 _day2

source_name: leaf_6pm_rep1 _day2

value: 6pm  day2


title: leaf_2pm _day2

description: Gene Expression at leaf_2pm_rep1 _day2

source_name: leaf_2pm_rep1 _day2

value: 2pm  day2


title: leaf_2am _day1

description: Gene Expression at leaf_2am_rep1 _day1

source_name: leaf_2am_rep1 _day1

value: 2am  day1


title: leaf_10pm _day2

description: Gene Expression at leaf_10pm_rep1 _day2

source_name: leaf_10pm_rep1 _day2

value: 10pm  day2


title: leaf_6am _day3

description: Gene Expression at leaf_6am_rep1 _day3

source_name: leaf_6am_rep1 _day3

value: 6am  day3


title: CO92_Cy5_YP1952_Cy3


title: CO92_Cy5_PestoidesA_Cy3

source_name: PestoidesA

value: PestoidesA


title: CO92_Cy5_PestoidesE_Cy3

source_name: PestoidesE

value: PestoidesE


title: CO92_Cy5_YP134AJ_Cy3


title: leaf_2am _day2

description: Gene Expression at leaf_2am_rep1 _day2

source_name: leaf_2am_rep1 _day2

value: 2am  day2


title: leaf_10am _day3

description: Gene Expression at leaf_10am_rep1 _day3

source_name: leaf_10am_rep1 _day3

value: 10am  day3


title: leaf_2pm _day3

description: Gene Expression at leaf_2pm_rep1 _day3

source_name: leaf_2pm_rep1 _day3

value: Leaf

value: 2pm  day3


title: CO92_Cy5_YP1670_Cy3


title: CO92_Cy5_YpTB11960_Cy3


title: CO92_Cy5_YpsD1_Cy3


title: CO92_Cy5_PestoidesD_Cy3

source_name: PestoidesD

value: PestoidesD


title: XO_hermaphrodite_L3_totalRNA_replicate1

city: Chapel Hill

first: Jason

last: Lieb

state: NC

address: 408 Fordham Hall, CB# 3280

department: Biology

institute: University of North Carolina at Chapel Hill

description: Gene expression data from L3 XO hermaphrodites.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.http://www.nimblegen.com/products/lit/index.html

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).

organism: Caenorhabditis elegans

source_name: L3 worms from TY2205

label_protocol: Cy3 Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html

growth_protocol: Worms were grown in standard S-basal media liquid culture. TY2205 (her-1(e1520) sdc-3(y126) V; xol-1(y9) X) were grown at 20C and bleached for embryos. Embryos were starved to L1, and filtered through 20uM Nitex memberane to remove dead embryos. L1s were fed and grown in 20C liquid culture until most were L3. Worms were collected and washed with M9 and PBS. Worms were resuspended in 1 pellet volume of PBS+ protease inhibitors (Calbiochem) and frozen as ÒpopcornÓ in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol: 1V sample (frozen powdered worm) in 10V Trizol that was stored at -80C was thawed at 37C. 1/5 V chloroform was added and vortexed for 30 seconds. After centrifugation at 13000 rpm for 5 minutes, aqueous phase containing RNA was recovered. RNA was precipitated by mixing with 0.8V isopropanol and incubation on ice, followed by centrifugation at 13000 rpm at 4C for 20 minutes. RNA was washed with 75% ethanol, dissolved in DEPC H2O and cleaned up using Qiagen RNeasy kit.

value: L3 larval stage


title: leaf_10pm _day3

description: Gene Expression at leaf_10pm_rep1 _day3

source_name: leaf_10pm_rep1 _day3

value: 10pm  day3


title: leaf_6pm _day3

description: Gene Expression at leaf_6pm_rep1 _day3

source_name: leaf_6pm_rep1 _day3

value: 6pm  day3


title: Germlineless_adult_totalRNA_replicate1

description: Gene expression data from young germlineless (glp-1) adults.

source_name: mixed stage embryos from N2

growth_protocol: Worms were grown in standard S-basal media liquid culture. JK1107 (glp-1(q224) III.) were grown at 15C and bleached for embryos. Embryos were starved to L1 and then fed and shifted to 25C. Germline-less adults were collected over 20uM Nitex membrane, and washed with M9 and PBS. Adults were resuspended in 1 pellet volume of PBS+ protease inhibitors (Calbiochem) and frozen as ÒpopcornÓ in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/.

value: young adults


title: GermlineContaining_adult_totalRNA_replicate2

description: Gene expression data from young feminized germline containing (fem-2) adults.

growth_protocol: Worms were grown in standard S-basal media liquid culture. DH245 (fem-2 (b245)) were grown at 15C and bleached for embryos. Embryos were starved to L1 and then fed and shifted to 23C. Adults were collected over 35uM Nitex membrane, and washed with M9 and PBS. Adults were resuspended in 1 pellet volume of PBS+ protease inhibitors (Calbiochem) and frozen as ÒpopcornÓ in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/.


title: Germlineless_adult_totalRNA_replicate2


title: CO92_Cy5_YP8908_Cy3


title: leaf_2am _day3

description: Gene Expression at leaf_2am_rep1 _day3

source_name: leaf_2am_rep1 _day3

value: 2am  day3


title: CO92_Cy5_YP1413_Cy3


title: ear_10pm_day1

description: Gene Expression at ear_10pm_rep1_day1

treatment_protocol: For Agilent microarray profiling, samples were taken starting at daybreak on day 1 (ZT0), and taken every 4 hours hence for 72 hours.  At each time point, the top-most immature ear, 4-5 cm in length, was collected from two separate plants to create one of three biological field replicates.

value: Immature Ear

value: 10pm day1


city: Boston

first: Henry

last: Lee

address: 36 Cummington St

department: Biomedical Engineering

institute: Boston University

description: Gene expression data for 1655 delta tnaA exposed to low levels of indole and norfloxacin, t2

hyb_protocol: Following fragmentation, biotinylated cDNA was hybridized to Affymetrix E. coli Antisense Genome arrays for 16h at 45C and 60rpm.

scan_protocol: Genechips were scanned at 532nm using an Affymetrix Gene Scanner 3000

data_processing: Data were normalized with FARMS and updated CDF (custom)

organism: Escherichia coli str. K-12 substr. MG1655

label_protocol: Biotinylated cDNA was prepared using an Enzo Bioarray Terminal Labeling Kit with Biotin-ddUTP.

growth_protocol: Continuous culture (0.48/hr) of MG1655∆tnaA in LB

extract_protocol: Total RNA was obtained using the RNEasy Protect Bacterial Mini Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: 50ng/mL norfloxacin, 200uM indole and 50ng/mL norfloxacin, 50ng/mL norfloxacin

tag: genotype/variation

value: tnaA knockout


description: Gene expression data for 1655 delta tnaA reexposed to low levels of norfloxacin, t3