title: Transition phase sample 1


title: Logarithmic phase sample 3

status: Public on Aug 08 2009

type: RNA

city: Tampa

first: James

middle: Timothy

last: Riordan

state: FL

address: 4202 E Fowler Ave BSF 218

department: CMMB

country: USA

institute: University of South Florida

description: There are probes on the array that target three different E. coli genomes. Those that were specific for genomes other than Sakai were excluded from the analysis.

hyb_protocol: Arrays were cross-linked by exposure to 600 mJ UV before blocking in 1% SDS, 5× SSC, and 1 mg/mL BSA at 42°C for 1 hour. After blocking, arrays were washed 2× 5 min in 0.1× SSC and 2× 30 s in H2O. Dried arrays were placed into hybridization cassettes (TeleChem International, Sunnyvale, Calif.) and the cDNA samples were suspended in 10 mM EDTA, denatured at 95°C for 5 min and then mixed with 40 uL of SlideHyb buffer 1 (Ambion) and loaded under a coverslip onto the array. Hybridizations were carried out at 47°C for 16–18 h. After hybridization, arrays were washed in 2× SSC, 0.5% SDS 37C for 5 min, followed by 2× 5 min in 0.1× SSC, 0.1% SDS 37°C, and then 2 × 2.5 min in room temperature 0.1× SSC. Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).

data_processing: The microarray data were analyzed using R (v. 2.2.1) and the MAANOVA (v. 0.98.8) package. Raw intensity values from replicate probes were averaged and log2 transformed after normalization with the pin-tip LOWESS method. The normalized intensity values were fitted to a mixed model ANOVA considering array and biological replicates as random factors and dye, strain and growth phase as fixed factors. The linear model tested was Y (intensity) = array + dye + strain (wild type or mutant) + growth phase (exponential or stationary) + strain*growth phase + sample (biological replicate) + error. Significant differences in expression due to strain, growth phase and strain*growth phase were determined using the Fs test in MAANOVA which uses a shrinkage estimator for gene-specific variance components that makes no assumption about the variances across genes with 500 random permutations to estimate the p-values. The q-value package in R was used for determining the false discovery rate (FDR).

molecule: total RNA

organism: Escherichia coli O157:H7 str. Sakai

source_name: rpoN mutant grown to logarithmic phase

label_protocol: Reverse transcription reactions contained 6ug RNA, 2ug random primers (Invitrogen, Carlsbad, Calif.), 1x first strand buffer (Invitrogen), 10mM DTT, 400U Superscript II (Invitrogen), 0.5mM each dATP, dCTP, and dGTP, 0.3mM dTTP, and 0.2mM amino-allyl dUTP. 30uL C. cDNA was purified using PCRreactions were incubated overnight at 42 cleanup columns (Qiagen) with Phosphate wash buffer (5mM K2HPO4, pH 8.0, 80%EtOH) and phosphate elution buffer (4mM K2HPO4, pH 8.5). Amino-allyl labeled cDNA was dried and resuspended in 0.1M sodium carbonate pH 9.3 and coupled with either Cy3 or Cy5 (Amersham Biosciences, Piscataway, N.J.). Uncoupled dye was removed by another purfication using the PCR cleanup kit. Concentration of cDNA and amount of incoporated dye was measured for each sample using a Nanodrop spectrophotometer (Ambion).

growth_protocol: EcJR-8 grown to OD600 = 0.5 in DMEM-MOPS 0.4% glucose at a 10:1 flask-to-media volume in a rotary shaker (180 RPM).

extract_protocol: 5mL of culture was mixed with 5mL of hot acid phenol:chloroform. Samples were held at 65ºC with periodic shaking for at least 10 minutes before centrifuging at 4000 rpm for 20 min. Supernatant was extracted again with acid-phenol:chloroform and then with chloroform:isoamyl alcohol (24.1). RNA was precipitated overnight at –80ºC in 2.5V 100% ethanol and 1/10V 3M sodium acetate pH 5.2. RNA samples were purified and treated with DNase using the Rneasy kit (Qiagen).

tag: genotype

value: rpoN mutant (EcJR-8)

tag: growth protocol

value: logarithmic phase in DMEM-MOPS

source_name: wild type grown to logarithmic phase

value: wild type


title: bWT.vehicle.replicate3

city: Davis

first: Michael

middle: L

last: Goodson

state: CA

address: One Shields Ave

institute: University of California Davis

description: TRb1 stably transformed cells treated with ethanol for 6h

hyb_protocol: Affymetrix GeneChip(r) Human Gene 1.0 ST arrays were hybridized to 2 ug of labeled, amplified single-stranded cDNA, washed, stained and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G

data_processing: The raw microarray data was normalized by the Robust Multichip Array (RMA) method using R 2.7.1 software and the affylmGUI 1.14.0 Bioconductor package.

label: biotin

organism: Homo sapiens

label_protocol: 200ng of total RNA were amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol (version 4)

growth_protocol: HepG2 transformants expressing ectopic TRa1, ectopic TRb1, or an empty plasmid control were generated as described in Chan IH et. al. (Oncogene. 2006 Jun 15;25(25):3576-88) using a G418 co-selection methodology.  Cell clones arising from individual transformation events were propagated and screened for integration and expression of the expression plasmid by PCR/reverse-transcriptase PCR.  Six, twelve, and eleven independent cell clones, scored as positive for the presence/expression of the introduced construct were pooled for the TRa1, TRb1, and empty plasmid control cell populations, respectively and used in the expression analysis.  HepG2 cells were maintained at 37°C in Dulbecco's Modified Eagle's Medium (DME) supplemented with 10% fetal bovine serum using bicarbonate buffer and a 5% CO2 atmosphere.

extract_protocol: The cells were harvested and the RNA was isolated using an RNeasy kit (Qiagen, Valencia CA).

treatment_protocol: The HepG2 transformant pools expressing ectopic TRa1, ectopic TRb1, or the empty plasmid control were treated with 100 nM T3 or with ethanol carrier alone for 6h in DMEM containing 10% hormone-stripped fetal bovine serum.

tag: cell line


title: aWT.100nMT3.replicate3

description: TRa1 stably transformed cells treated with T3 for 6h


title: bWT.100nMT3.replicate1

description: TRb1 stably transformed cells treated with T3 for 6h


title: NR.vehicle.replicate1

description: Empty plasmid control stably transformed cells treated with ethanol for 6h


title: Logarithmic phase sample 4

scan_protocol: Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).


title: Logarithmic phase sample 2


title: p0 v. p1 rep4

city: East Lansing

first: Linda

middle: S.

last: Mansfield

state: MI

address: 181 Food Safety Bldg.

department: Microbiology and Molecular Genetics

institute: Michigan State University

hyb_protocol: Dyed samples to be compared were combined and resuspended in 196µl Ambion SlideHyb buffer 1.  Samples were added to Agilent gasket slides, sandwiched with a UV-crosslinked, blocked microarray slide and sealed inside an Agilent hybridization chamber.  This was rotated at 54 degrees celsius for 18 hours to allow hybridization to the array before washing and scanning.

scan_protocol: Slides were scanned using a GenePix scanner and GenePix Pro 4.1 software.  PMT values were adjusted to obtain approximately equal levels of signal from both wavelength channels.

data_processing: Done using R/LIMMA.  Signal ratios were normalized using a global loess procedure.  A least squares linear model was fit, and using false-discovery rate adjustment, P-values less than 0.05 were considered differentially expressed.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Unpassaged Camylobacter jejuni 11168 RNA

label_protocol: 6µg RNA was reverse transcribed with random hexamer primers and an aminoallyl-dUTP/dNTP mix using Invitrogen SuperScriptIII  CyDyes 3 or 5 from New England Biolabs were used to dye aminoallyl-cDNA samples.  Reactions were cleaned at each step using a QIAGEN QIAquick kit.

growth_protocol: C. jejuni strains were grown in jars with atmospheric gas exchanged for a 10% CO2, 10% H2, 80% N2 in Bolton broth in 25cm2 tissue culture flasks.  Jars were shaken at 80 rpm, 37 degrees Celsius for 18 hours, at which point the bacteria has reached mid-stationary phase growth.

extract_protocol: Contents of C. jejuni broth cultures were poured into 15ml tubes containing 0.1 volume of cold RNA “stop solution” consisting of 1:10 volumes of saturated phenol:ethanol.  This was centrifuged at 5000rpm, 4 degrees Celsius for 20 minutes to pellet cells.  RNA was extracted by lysing C. jejuni with 200µl 1mg/ml lysozyme solution supplemented with 20µl Proteinase K, followed by RNA isolation with QIAGEN RNeasy kit (following manufacturer's instructions).  On column DNase digestion was done twice.  Total RNA was ethanol precipitated overnight before determining RNA quality and concentration using the NanoDrop, PCR for DNA detection, and the Agilent 2100 BioAnalyzer.

tag: adaptation status

value: Unadapted (unpassaged in C57 BL/6 IL-10-/- mice)

source_name: Passaged Camylobacter jejuni 11168 RNA

value: Adapted:1 passage in C57 BL/6 IL-10-/- mice


title: bWT.vehicle.replicate1

source_name: TRb1 stably transformed cells treated with ethanol for 6h


title: bWT.vehicle.replicate2


title: aWT.100nMT3.replicate2

source_name: TRa1 stably transformed cells treated with T3 for 6h


title: HepG2 Pool_60

status: Public on Aug 13 2009

city: Woodbury

first: Chris

last: Zaleski

state: NY

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Labs

description: single chip, 1 replicate

hyb_protocol: 2 micrograms of  double-stranded cDNA were labeled and hybridized to Affymetrix tiling arrays containing probes against non-repepetitive portions of human chromosomes 21 and 22 essentially as described in Kapranov et al, Science. 2007 Jun 8;316(5830):1484-8.

scan_protocol: Arrays were scanned on Affymetrix GCS3000 scanner

data_processing:
See supplement materials of Djebali, S, et al (2009) Nature in press
Number Sequences: 10, Data: signal, Scale: Linear, AlgName: TAS, AlgVersion: 1.1.01, probe_coordinate_convention: 0_indexed_center

label: Biotin

molecule: polyA RNA

source_name: BD SMARTTM RACE cDNA – HepG2

label_protocol: 2 micrograms of polyA+ RNA were converted into double-stranded cDNA essentially as described in Kapranov et al, Science. 2007 Jun 8;316(5830):1484-8.

growth_protocol: 11 tissues poly A+ RNA was purchased and 5 cell lines were grown as suggested by ATCC

extract_protocol: see Kapranov, et al Science 2002

tag: tissue

value: HepG2 cell line


title: Logarithmic phase sample 1


title: aWT.100nMT3.replicate1


title: p0 v. p1 rep2


title: aWT.vehicle.replicate1

description: TRa1 stably transformed cells treated with ethanol for 6h


title: p0 v. p1 rep3


title: Mouses bone marrow treated with hRANKL 72h

city: Tokyo

first: Masamichi

last: Takami

address: 1-5-8, Hatanodai, Shinagawa

department: School of Dentistry

country: Japan

institute: Showa University

description: Osteoclastogenesis

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Mus musculus

source_name: bone marrow cells

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

growth_protocol: Mouse (C57/BL6) bone marrow cells were harvested and cultured in the presence of hM-CSF (50 ng/ml) for 3 days to induce macrophages.

extract_protocol: RNeasy mini kit (Quiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Macrophages were treated with hRANKL (150 ng/ml) for 0, 24, and 72 h.

tag: development stage

value: Osteoclast

tag: strain

tag: time

value: 72 hr


title: aWT.vehicle.replicate3

source_name: TRa1 stably transformed cells treated with ethanol for 6h


title: Brown eye color pool - cohort 1

type: genomic

city: Brisbane

first: Stuart

last: Macgregor

state: Queensland

address: 300 Herston Road

department: Genetic Epidemiology

country: Australia

description: Pool of 100 individuals

hyb_protocol: Array data. SNPs were genotyped on pool samples using Illumina arrays. Arrays were treated according to standard protocols.

scan_protocol: Arrays were scanned at Queensland Institute of Medical Research.

data_processing:
Raw probe intensities were dumped from Illumina array software and analysed using methods described in Macgregor et al Nucleic Acids Research, 2006, Vol. 34, No. 7 e55.
Bead-level intensity data were analyzed. SNPs with beadscore values <-50 were excluded. Copy number variants and SNPs from the sex chromosomes were not analyzed. SNPs were also removed in the initial quality control if they had a minor allele frequency <1% in the HapMap CEU reference samples. SNPs from Illumina TOP strand exhibited different levels of pooling error to SNPs from Illumina BOTTOM strand, hence only 261887 (HumanHap550) and 375246 (1M) SNPs from the ‘BOTTOM’ strand are included in the final analysis (in estimated pooling frequencies).

label: Cy3, Cy5

molecule: genomic DNA

source_name: Brown eye color - pool of 100 individuals

label_protocol: The Infinium assay used on the Illumina arrays is based on allele-specific single base extension using two color labeling with the Cy3 and Cy5 fluorescent dyes

extract_protocol: Blood samples from individuals from each phenotype definition were pooled. A single extraction was performed on each blood pool. Extraction was done according to manufacturers guidelines using the QIA-AMP DNA blood maxi kit (QIAGEN, Valencia, CA, USA). The extracted DNA was quantified by spectrophotometry.

value: blood


title: Veg 16S rRNA analysis

status: Public on Aug 07 2009

type: other

city: Montreal

first: Etienne

last: Yergeau

state: Qc

address: 6100 Royalmount Ave

department: Environmental Microbiology

country: Canada

institute: NRC-BRI

description: 16S rRNA analysis

hyb_protocol: Slides were pre-hybridized for 1 h at 37°C with a DIG easy hybridization solution (Roche Applied Science, Laval, QC, Canada) containing 5% BSA. Samples were then assigned randomly to a sub-array and hybridization was carried out for approximately 20 h at 37°C on a Slide Booster apparatus (Implen, Calabasas, CA). Slides were washed three times for 5 minutes at 37°C in 0.1X SSC / 0.1% SDS followed by a single wash for 5 minutes at 37°C in 0.1X SSC.

scan_protocol: Slides were scanned in a ScanArray GX PLUS Microarray Scanner (Perkin-Elmer, Boston, MA) at a resolution of 10 µm.

data_processing: Images were transferred to QuantArray (Perkin-Elmer) where each spot was identified and quantified. Data was then exported to Excel where net spot intensity was calculated by subtracting the background signal from the target spot intensity. A spot was scored as “present” if its net intensity was at least 3 times higher than the median net intensity of all spots. For a taxon to be scored as present, all of its triplicate spots had to be scored as present. The results from the 16S rRNA gene microarray were only used in the binary form (presence/absence of taxa).

molecule: other

organism:
Bacteria
Archaea

source_name: Alert

label_protocol: Total RNA extracted from all soil samples (N=38) was submitted to an RT-PCR procedure with eubacterial 16S rRNA gene primers F1-R13 using the QIAGEN OneStep RT-PCR Kit (QIAGEN, Valencia, CA), following the manufacturer’s instruction (except that all volumes were halved), at an annealing temperature of 50°C. RT-PCR products were then chemically labeled using the Label IT nucleic acid labeling kit (Mirus Bio, Madison, WI).

extract_protocol: Soil DNA was extracted from a 0.5g soil sub-sample using the MoBio DNA Power Soil kit (MoBio Laboratories, Carlsbad, CA), while soil RNA was extracted from a 2.0g soil sub-sample using the MoBio RNA Power Soil kit. Residual DNA in RNA extracts was removed using the Turbo DNA-free kit (Ambion, Austin, TX).

tag: year

tag: sample

value: Vegetated


title: Bio Contro 16S rRNA analysis

description: 16S rRNA analysis

value: Biopile control


title: p0 v. p1 rep1


title: LC1 16S rRNA analysis

description: 16S rRNA analysis

tag: contamination status

value: hydrocarbon contaminated


title: Poly  16S rRNA analysis

description: 16S rRNA analysis

value: Polygons


title: NFNT 16S rRNA analysis

description: 16S rRNA analysis

value: NF-NT


title: Mouses bone marrow treated with hRANKL 24 h

description: Osteoclastogenesis

value: Differentiating precursor

value: 24 hr


title: Bio-6 16S rRNA analysis

description: 16S rRNA analysis


title: Mouses bone marrow treated with hRANKL 0 hr

description: Osteoclastogenesis

value: Precursor

value: 0 hr


title: Blue eye color pool - cohort 1

institute: Queensland Institute of Medical Research

description: Pool of 100 individuals

source_name: Blue eye color - pool of 100 individuals


title: NC 16S rRNA analysis

description: 16S rRNA analysis

value: NC


title: BZNT 16S rRNA analysis

description: 16S rRNA analysis

value: BZ-NT


title: aWT.vehicle.replicate2


title: Bio3 1y 16S rRNA analysis

description: 16S rRNA analysis

tag: bioremediation treatment

value: Alert (ex situ)


title: Bio1 1y 16S rRNA analysis

description: 16S rRNA analysis


title: Bio4 1y 16S rRNA analysis

description: 16S rRNA analysis


title: Bio2 1y 16S rRNA analysis

description: 16S rRNA analysis


title: Age-related macular degeneration pool - cohort 2

description: Pool of 131 individuals

source_name: Age-related macular degeneration - pool of 131 individuals


title: Pseudoexfoliation syndrome pool - cohort 3

description: Pool of 100 individuals

source_name: Pseudoexfoliation syndrome - pool of 100 individuals


title: Healthy controls pool - cohort 3

description: Pool of 216 individuals. This entry has identical raw data as that deposited in GSM437638. The composition of the allelle frequency table is different from that reported in GSM437638 because the data was analyzed in separate cohorts.

source_name: Healthy Controls - pool of 216 individuals


title: Bio4 1m 16S rRNA analysis

description: 16S rRNA analysis


title: Bio3 1m 16S rRNA analysis

description: 16S rRNA analysis


title: Bio2 1m 16S rRNA analysis

description: 16S rRNA analysis


title: CompA 16S rRNA analysis

description: 16S rRNA analysis

value: Composite A


title: 33D 16S rRNA analysis

description: 16S rRNA analysis

source_name: Eureka


title: CompB 16S rRNA analysis

description: 16S rRNA analysis

value: Composite B


title: 35B 16S rRNA analysis

description: 16S rRNA analysis


title: 4A 4y 16S rRNA analysis

description: 16S rRNA analysis

value: Eureka (in situ)


title: 23S 16S rRNA analysis

description: 16S rRNA analysis


title: 2A 4y 16S rRNA analysis

description: 16S rRNA analysis


title: Bio1 1m 16S rRNA analysis

description: 16S rRNA analysis


title: 3A 4y 16S rRNA analysis

description: 16S rRNA analysis


title: 6A 1m 16S rRNA analysis

description: 16S rRNA analysis


title: 5A 1m 16S rRNA analysis

description: 16S rRNA analysis


title: Healthy controls pool - cohort 2

description: Pool of 216 individuals. This entry has identical raw data as that deposited in GSM437640. The composition of the allelle frequency table is different from that reported in GSM437640 because the data was analyzed in separate cohorts.


title: 9A 3y 16S rRNA analysis

description: 16S rRNA analysis


title: 9A 5y 16S rRNA analysis

description: 16S rRNA analysis


title: 32D 16S rRNA analysis

description: 16S rRNA analysis


title: 1A 4y 16S rRNA analysis

description: 16S rRNA analysis


title: 4A 1y 16S rRNA analysis

description: 16S rRNA analysis


title: 9A T0 16S rRNA analysis

description: 16S rRNA analysis


title: 1A 1y 16S rRNA analysis

description: 16S rRNA analysis


title: 2A 1y 16S rRNA analysis

description: 16S rRNA analysis


title: 3A 1m 16S rRNA analysis

description: 16S rRNA analysis


title: 4A 1m 16S rRNA analysis

description: 16S rRNA analysis


title: 3A 1y 16S rRNA analysis

description: 16S rRNA analysis


title: Poly

description: experimental sample compared to reference DNA (lambda phage)

hyb_protocol: The concentrated labeled DNA was resuspended in a final volume of 30 µL of DIG Easy Hyb hybridization buffer (Roche Diagnostics, Laval, Quebec) containing 10 µg each of salmon sperm DNA (Sigma-Aldrich, St-Louis, MO) and tRNA (Sigma-Aldrich). Lambda genomic DNA, used as PC, was labeled with Cy3 and 100 ng of this Cy3-lambda (PC) was added to each sample probe labeled with Cy5, before the hybridization. The hybridization mixture was heated at 95°C for 2 min to denature the DNA, and after a quick spin was introduced by capillarity under the LifterSlip covering the pre-hybridized microarray. The slides were incubated at 50°C for 16-20 h in a water bath within hybridization chambers. The slides were washed three times in 0.1X SSC and 0.1% SDS for 10 min at 50°C with agitation in a Belly Dancer (Stovall Life Science Inc., Greensboro, NC). Then the slides were rinsed three times in 0.1X SSC, three times in isopropanol, and dried by spinning in a slide microspin.

scan_protocol: The DNA microarray slides were scanned in a ScanArray Lite (Perkin Elmer, Boston, MA) upgraded with ScanArray Express (version 2.2.0.22) at 10 µm resolution.  Lasers at 543 nm and 633 nm were used to excite the Cy3 and Cy5 dyes, respectively.  The resulting 16-bit TIFF files were quantified using ScanArray Express.

data_processing: The intensity of each spot was measured with ScanArray Express using the histogram quantitation method; the percentile ranges for histograms were 80% for low signal range, 95% for high signal range, 5% for low background range and 20% for high background range. The median intensity minus the median background intensity was used for further calculations performed in Microsoft Excel. The background measurement refers to the local spot background intensity. Prior to normalization, all spots with a Signal-to-Noise ratio (SNR) lower than 3 were removed. The SNR was calculated using the following formula: (Median Signal – Median Background)/Standard Deviation of Background. Normalization between each array was performed using an internal labeling control (IC) consisting of a 290 bp luxA fragment. This fragment was added to each labeling reaction at a ratio of 0.05% of the DNA to be labeled. The intensity of each Cy5-sample gene spot  was corrected using the average intensity of all Cy3-lambda signals. Corrected intensity values were averaged over triplicate spots to give a single value per gene. The intensity of the genes for which hybridization of the probes could not be visually detected in image analysis was set to zero. Relative intensity values were then calculated by dividing the intensity of a gene by the sum of the intensity for all genes (excluding controls). This “relative abundance” represents the fraction of the total intensity that is due to a particular gene and this value was subsequently used in statistical analyses.

label_protocol: Hybridizations were carried out for all samples (N=38) with 100 ng of genomic DNA labeled with Cy5 using the BioPrime Array CGH Genomic Labeling kit (Invitrogen, Carlsbad, CA).

extract_protocol: Soil DNA was extracted from a 0.5g soil sub-sample using the MoBio DNA Power Soil kit (MoBio Laboratories, Carlsbad, CA).

organism: Escherichia coli

source_name: Lambda phage

tag: phage

value: Lambda


title: 1A T0 16S rRNA analysis

description: 16S rRNA analysis


title: Bio-6


title: NFNT


title: Bio Contro


title: NC


title: Veg


title: Bio3 1y


title: Bio2 1y


title: LC1


title: Bio4 1m


title: Bio3 1m


title: Bio1 1y


title: CompB


title: Bio1 1m


title: Bio4 1y


title: BZNT


title: CompA


title: 23S


title: 35B


title: 32D


title: 9A 5y


title: 33D


title: 3A 4y


title: 4A 4y


title: 9A 3y


title: 1A 4y


title: 2A 4y


title: 6A 1m


title: 5A 1m


title: 4A 1y


title: 3A 1y


title: Bio2 1m


title: 4A 1m


title: 1A T0


title: 3A 1m


title: 2A 1y


title: 9A T0


title: 1A 1y


title: Geldanamycin_HD vs HD+GA_3000209227_L

city: São Paulo

first: Cesar

middle: Moises

last: Camilo

state: SP

address: Av. Prof. Lineu Prestes

department: Departamanto de Bioquímica

country: Brazil

institute: Instituto de Química - USP

description: Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in Cy3 and Cy5 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless,. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the heat shock time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((cy3+cy5)/2)].

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were shrinked in water for 10s and dried with nitrogen gas.

scan_protocol: Microarray slides were scanned with a Generation III DNA Scanner (Amersham Biosciences).

data_processing: filtering low intensity spots, LOWESS normalization.

organism: Blastocladiella emersonii

label_protocol: 10ug of total RNA was reverse transcribed and labeled using “Superscript® Plus Indirect cDNA Labeling System” (Invitrogen®). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.

extract_protocol: total RNA was extracted using Trizol regent (Invitrogen)

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air) and then submitted to 1-hour hypoxia (1%sat. O2 in air)

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air), treated with 2 µM of geldanamycin and then submitted to 1-hour hypoxia (1%sat. O2 in air)


title: Geldanamycin_HD vs HD+GA_3000209222_L


title: Geldanamycin_HD vs HD+GA_3000209226_R


title: Geldanamycin_HD vs HD+GA_3000209226_L


title: Geldanamycin_HD vs HD+GA_3000209222_R


title: Geldanamycin_HD vs HD+GA_3000209225_L


title: Geldanamycin_HD vs HD+GA_3000209221_L


title: Geldanamycin_HD vs HD+GA_3000209227_R


title: Geldanamycin_HD vs HD+GA_3000209225_R


title: Gradual_C70 vs C70r_3000209710_R

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air), submitted to 35%, 17.5%, 5%, 1%, 0% and then restored to normoxia (70% sat. O2), for 1 hour each.


title: Gradual_C70 vs C70r_3000209718_R

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air)


title: Geldanamycin_self_self_3000209224_R


title: Gradual_C70 vs C70r_3000209706_R


title: Gradual_C70 vs C0_3000209720_R

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air), submitted to 35%, 17.5%, 5%, 1% and then to 0% sat. O2, for 1 hour each.


title: Gradual_C70 vs C0_3000209720_L


title: Gradual_C70 vs C70r_3000209706_L


title: Geldanamycin_self_self_3000209223_L


title: Geldanamycin_HD vs HD+GA_3000209221_R


title: Gradual_C70 vs C70r_3000209718_L


title: Gradual_C70 vs C0_3000209738_L


title: Geldanamycin_self_self_3000209224_L


title: Geldanamycin_HD vs HD+GA_3000209220_L


title: Geldanamycin_self_self_3000209223_R


title: Gradual_C70 vs C0_3000209738_R


title: Geldanamycin_HD vs HD+GA_3000209220_R


title: Gradual_C70 vs C70r_3000209710_L


title: Gradual_C70 vs C1_3000209721_R

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air), submitted to 35%, 17.5%, 5% and then to 1% sat. O2, for 1 hour each.


title: Gradual_C70 vs C0_3000209711_L


title: Gradual_C70 vs C5_3000209201_R

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air), submitted to 35%, 17.5% and then to 5% %sat. O2, for 1 hour each.


title: Gradual_C70 vs C1_3000209721_L


title: Gradual_C70 vs C1_3000209709_R


title: Gradual_C70 vs C1_3000209714_R


title: Gradual_C70 vs C1_3000209714_L


title: Gradual_C70 vs C5_3000209704_L


title: Gradual_C70 vs C5_3000209704_R


title: Gradual_C70 vs C5_3000209713_L


title: Gradual_C70 vs C5_3000209713_R


title: Gradual_C70 vs C1_3000209709_L


title: Gradual_C70 vs C5_3000209201_L


title: Gradual_C70 vs C17.5_3000209723_L

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air), submitted to 35% sat. O2 for 1 hour and then to 17.5% sat. O2 for 1 hour


title: Gradual_C70 vs C17.5_3000209723_R


title: Gradual_C70 vs C17.5_3000209712_R


title: Gradual_C70 vs C17.5_3000209200_L


title: Gradual_C70 vs C35_3000209716_R

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air) and then submitted to 35% sat. O2


title: Gradual_C70 vs C17.5_3000209200_R


title: Gradual_C70 vs C35_3000209716_L


title: Gradual_C70 vs C35_3000209707_R


title: Gradual_C70 vs C35_3000209705_R


title: Gradual_C70 vs C35_3000209707_L


title: self_self_3000209726_R


title: Rich media (after osmotic stress), t45 min

city: Rehovot

first: Amir

last: Mitchell

address: Hertzel

country: Israel

institute: Weizmann Inst.

description: Gene expression in rich media (after priming 45 min in osmotic stress), 45min

hyb_protocol: According to standard Affymetrix protocol

data_processing: RMA algorithms using bioconductor software implemented in R

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cells transferred to rich media after priming in osmotic stress

label_protocol: cDNA was prepared using poly(T) primers, labeled cRNA was prepared according to standard Affymetrix protocol.

growth_protocol: Cells were grown in YPD to mid log phase in 30 degrees

extract_protocol: Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)

treatment_protocol: At time 0 cells were treated with mild stresses and then transftered to another stress

tag: stress

value: osmotic stress followed by transfer to rich media

value: 45 min


title: Gradual_C70 vs C17.5_3000209712_L


title: DPY_T0 vs T1h_3000209243_L

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air) and then treated with 150 µM of 2,2´-dipyridyl for 1 hour.


title: Gradual_C70 vs C35_3000209705_L


title: self_self_3000209708_L


title: Rich media (after osmotic stress), t15 min

description: Gene expression in rich media (after priming 45 min in osmotic stress), 15min

scan_protocol: According to standard Affymetrix protocol

value: 15 min


title: Oxidative stress (after osmotic stress), t45 min

description: Gene expression in H2O2 0.66mM (after priming 45 min in osmotic stress), 45min

source_name: H2O2 treated S. cerevisiae cells after priming in osmotic stress

value: osmotic stress followed by oxidative stress


title: self_self_3000209708_R


title: Oxidative stress (after osmotic stress), t90 min

description: Gene expression in H2O2 0.66mM (after priming 45 min in osmotic stress), 90min

value: 90 min


title: Oxidative stress (after osmotic stress), t15 min

description: Gene expression in H2O2 0.66mM (after priming 45 min in osmotic stress), 15min


title: Rich media (after heat shock), t15 min

description: Gene expression in rich media (after priming 45 min in heat shock), 15min

source_name: S. cerevisiae cells transferred to rich media after priming in heat shock

value: heat stress followed by transfer to rich media


title: Oxidative stress (after osmotic stress), t30 min

description: Gene expression in H2O2 0.66mM (after priming 45 min in osmotic stress), 30min

value: 30 min


title: DPY_T0 vs T1h_3000209216_L


title: Direct_C70 vs C70r_1h_3000209214_R

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air), submitted to 5-hour hypoxia (1%sat. O2 in air) and then reoxygenated to normoxia (70%sat. O2 in air) for 1 hour.


title: Direct_C70 vs C70r_1h_3000209212_R


title: DPY_T0 vs T1h_3000209215_R


title: self_self_3000209726_L


title: Direct_C70 vs C70r_1h_3000209213_L


title: DPY_T0 vs T1h_3000209243_R


title: DPY_T0 vs T1h_3000209216_R


title: DPY_T0 vs T1h_3000209215_L


title: Direct_C70 vs C70r_1h_3000209212_L


title: Direct_C70 vs C70r_1h_3000209214_L


title: Rich media (after heat shock), t45 min

description: Gene expression in rich media (after priming 45 min in heat shock), 45min


title: Direct_C70 vs C70r_1h_3000209213_R


title: Oxidative stress, t90 min

description: Gene expression in H2O2 0.66mM, 90min

source_name: H2O2 treated S. cerevisiae cells

value: oxidative stress


title: Oxidative stress (after heat shock), t90 min

description: Gene expression in H2O2 0.66mM (after priming 45 min in heat shock), 90min

source_name: H2O2 treated S. cerevisiae cells after priming in heat shock

value: heat stress followed by oxidative stress


title: Oxidative stress (after heat shock), t45 min

description: Gene expression in H2O2 0.66mM (after priming 45 min in heat shock), 45min


title: Oxidative stress, t45 min

description: Gene expression in H2O2 0.66mM, 45min


title: Direct_C70 vs C1_5h_3000209210_R

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air) and then submitted to 5-hour hypoxia (1%sat. O2 in air)


title: Oxidative stress, t30 min

description: Gene expression in H2O2 0.66mM, 30min


title: Direct_C70 vs C1_5h_3000209211_L

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air)


title: Oxidative stress (after heat shock), t30 min

description: Gene expression in H2O2 0.66mM (after priming 45 min in heat shock), 30min


title: Osmotic stress, t45 min

description: Gene expression in KCl 0.8M, 45min

source_name: KCl treated S. cerevisiae cells

value: osmotic stress


title: Direct_C70 vs C1_5h_3000209209_L


title: Oxidative stress (after heat shock), t15 min

description: Gene expression in H2O2 0.66mM (after priming 45 min in heat shock), 15min


title: Oxidative stress, t15 min

description: Gene expression in H2O2 0.66mM, 15min


title: Direct_C70 vs C1_5h_3000209211_R


title: Direct_C70 vs C1_5h_3000209210_L


title: Direct_C70 vs C1_1h_3000209703_L

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air) and then submitted to 1-hour hypoxia (1%sat. O2 in air)


title: Gradual_C70 vs C0_3000209711_R

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air), submitted to 35%, 17.5%, 5%, 1% and then to 0% sat. O2, for 1 hour each.


title: Direct_C70 vs C1_1h_3000209703_R


title: Direct_C70 vs C1_5h_3000209209_R


title: Osmotic stress, t30 min

description: Gene expression in KCl 0.8M, 30min


title: Direct_C70 vs C1_1h_3000209702_R


title: WM276

city: Birmingham

first: Robin

last: May

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: Single isolate vs. pooled isolates.

hyb_protocol: 65 degrees C for 17 hours.

scan_protocol: 5um resolution, 100% PMT.

data_processing: Probe values were extracted using Agilent Feature Extraction software 9.5.3.1.

organism: Cryptococcus bacillisporus

source_name: C. gattii WM276 grown in J774 macrophages for 24hrs

label_protocol: Labelling was conducted using the Agilent Two-Colour Microarray-Based Gene Expression Analysis protocol, Version 5.5, February 2007.

growth_protocol: C. gattii strains were grown overnight in broth and then used to infect J774 mouse macrophage cells. Extracellular yeast were washed off and intracellular yeast allowed to grow for 24hrs.

extract_protocol: Yeast RNA was isolated using the Invitrogen Micro-to-Midi kit, in accordance with the manufacturer's instructions.

treatment_protocol: Host macrophages were lysed by 20 minute exposure to water.  C. gattii cells were isolated by centrifugation and washed once in 0.05% SDS to remove macrophage RNA.

source_name: Pooled RNA, using equal quantities from each of the 23 samples

value: mixed


title: CBS6956

description: Single isolate vs. pooled isolates.

source_name: C. gattii CBS6956 grown in J774 macrophages for 24hrs


title: CBS10089

description: Single isolate vs. pooled isolates.

source_name: C. gattii CBS10089 grown in J774 macrophages for 24hrs


title: CBS8684

description: Single isolate vs. pooled isolates.

source_name: C. gattii CBS8684 grown in J774 macrophages for 24hrs


title: CBS10485

description: Single isolate vs. pooled isolates.

source_name: C. gattii CBS10485 grown in J774 macrophages for 24hrs


title: Direct_C70 vs C1_1h_3000209702_L


title: Untreated, t0_b

description: Gene expression in Rich media (reference sample)

source_name: Untreated S. cerevisiae cells

value: untreated

value: 0 min


title: Heat shock, t45 min

description: Gene expression in heat shock 40deg, 45min

source_name: heat treated S. cerevisiae cells

value: heat stress

value: 45 min


title: A1M-R406

description: Single isolate vs. pooled isolates.

source_name: C. gattii A1M-R406 grown in J774 macrophages for 24hrs


title: Heat shock, t30 min

description: Gene expression in heat shock 40deg, 30min


title: A1M-R271

description: Single isolate vs. pooled isolates.

source_name: C. gattii A1M-R271 grown in J774 macrophages for 24hrs


title: FoxM1 siRNA transfected Human aortic vascular smooth muscle cells

city: Cincinnati

first: I-Ching

last: Wang

state: OH

address: 3333 Burnet Ave.

department: Pulmonary Biology

institute: CCHMC

description: HAVSMC transfected FoxM1 siRNA for 48hours

hyb_protocol: Following fragmentation, 10 ug cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA was prepared according to standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human aortic vascular smooth muscle cells were cultured on 100mm plates in a single layer, and replated cell 24 hr before siRNA transfection.

extract_protocol: RNAstat-60 extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Human aortic vascular smooth muscle cells were transfected with 100nM of siRNA targeting human FoxM1 or non-targeting control using Invitrogen Lipofectamine 2000 reagent.  After 48 hr culture, cells were harvested using RNAstat-60.

value: aorta

tag: cell type

value: vascular smooth muscle cells

tag: genome/variation

value: FoxM1 siRNA knock-down


title: A1M-F2866

description: Single isolate vs. pooled isolates.

source_name: C. gattii A1M-F2866 grown in J774 macrophages for 24hrs


title: K562 Pool_2

description: single chip, 1 replicate

source_name: BD SMARTTM RACE cDNA – K562

value: K562 cell line


title: Direct_C70 vs C1_1h_3000209701_R

description: Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in Cy3 and Cy5 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless,. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the heat shock time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((cy3+cy5)/2)].


title: Untreated, t0_a


title: RB14

description: Single isolate vs. pooled isolates.

source_name: C. gattii RB14 grown in J774 macrophages for 24hrs


title: control siRNA transfected Human aortic vascular smooth muscle cells

description: HAVSMC transfected control siRNA for 48hours


title: ENV131

description: Single isolate vs. pooled isolates.

source_name: C. gattii ENV131 grown in J774 macrophages for 24hrs


title: 56A

description: Single isolate vs. pooled isolates.

source_name: C. gattii 56A grown in J774 macrophages for 24hrs


title: LA362

description: Single isolate vs. pooled isolates.

source_name: C. gattii LA362 grown in J774 macrophages for 24hrs


title: A1M-R376

description: Single isolate vs. pooled isolates.

source_name: C. gattii A1M-R376 grown in J774 macrophages for 24hrs


title: tissue_30days_4

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

description: RNA integrity tested with Bioanalyzer (Agilent)

hyb_protocol: Affymetrix standards

scan_protocol: Affymetrix standards

data_processing: RMA normalization, log2 transformed

source_name: skin tissue

label_protocol: Affymetrix standards

extract_protocol: RNeasy Fibrous Tissue Mini Kit (Qiagen)

tag: age

value: 30 days old

value: C57 DBA FVB mixed

value: skin


title: CBS10090

description: Single isolate vs. pooled isolates.

source_name: C. gattii CBS10090 grown in J774 macrophages for 24hrs

source_name: Pooled RNA, using equal quantities from each of the 23 samples


title: tissue_30days_5


title: RB50

description: Single isolate vs. pooled isolates.

source_name: C. gattii RB50 grown in J774 macrophages for 24hrs


title: NHS_ct_c

first: Bruce

middle: J

last: Aronow

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer.  Heat hybridization cocktail to 99C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol EukGE-WS2v5_450. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing: GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.1. Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between 1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly. GeneSpring 7.3.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering.

source_name: Normal Human Skin

label_protocol: Samples used for hybridization consisted of non-pooled (NP) RNA extracts from biopsies of cultured skin substitutes taken at multiple time points during in vitro incubation/maturation and after grafting to full thickness wounds on athymic mice.  The Genechip Expression 3 Amplification One-Cycle Target Labeling and Control Reagents Kit (Affymetrix) was used to prepare biotin-labeled fragmented cRNA. Specifically, the One-Cycle cDNA Synthesis Kit (Affymetrix) was used to make double-stranded cDNA from total RNA. An in vitro transcription reaction using the IVT Labeling Kit (Affymetrix) created biotin-labeled cRNA target. The cRNA target was chemically fragmented and then hybridized to an Affymetrix Human U133 plus 2.0 gene chip.

extract_protocol:
Biopsies of normal adult female breast skin, or CSS in vitro, or CSS in vivo, were used for preparation of total RNA using the RNeasy Mini Kit (QIAGEN, Inc., Valencia, CA) followed by further purification using phenol and chloroform extraction and ethanol precipitation.
Quality control steps: RNA quality was analyzed using the Agilent Bioanalyzation system (Agilent Technologies, Inc., Palo Alto, CA), to ensure the integrity of the RNA.  A total of 3 samples per time point, representing the highest quality RNA preparations and at least one sample from each skin donor, were selected; due to RNA degradation, only 2 samples were available for the day 3 in vitro and day 56 in vivo time points.

treatment_protocol: Biopsies for RNA analysis were collected from cultured human skin substitutes at culture days 3, 7, or 14 in vitro, or 3, 7, 14, 28, 42, or 56 after orthotopic transplantation to athymic (nude) mice.

value: normal human skin obtained incidental to breast or abdomen reduction surgery

tag: source

value: genetically-unrelated individual 4


title: tissue_newborn_2

growth_protocol: Primary keratinocytes were obtained from newborn mice as described in Santos et al J Biol Chem 277, 19122 (2002). Pooled cells from five different mice of same genotype were cultured in low Ca2+ medium for no longer that 3 days without passage.

value: newborn

value: FVB


title: CBS7750

description: Single isolate vs. pooled isolates.

source_name: C. gattii CBS7750 grown in J774 macrophages for 24hrs


title: NHS_ct_b

value: genetically-unrelated individual 3


title: ICB184

description: Single isolate vs. pooled isolates.

source_name: C. gattii ICB184 grown in J774 macrophages for 24hrs

value: mixed


title: A1M-F3016

description: Single isolate vs. pooled isolates.

source_name: C. gattii A1M-F3016 grown in J774 macrophages for 24hrs


title: A1M-R272

description: Single isolate vs. pooled isolates.

source_name: C. gattii A1M-R272 grown in J774 macrophages for 24hrs


title: tissue_30days_2


title: tissue_30days_3


title: ENV152

description: Single isolate vs. pooled isolates.

source_name: C. gattii ENV152 grown in J774 macrophages for 24hrs


title: inVitro_3_a

value: cultured skin substitute

tag: incubation

value: in vitro

tag: culture days


title: tissue_newborn_1


title: NHS_ct_a

value: genetically-unrelated individual 1


title: tissue_30days_1


title: NHS_ct_d

value: genetically-unrelated individual 2


title: inVitro_3_b


title: inVivo_42_c


title: A1M-R265

description: Single isolate vs. pooled isolates.

source_name: C. gattii A1M-R265 grown in J774 macrophages for 24hrs


title: Cells_newborn_5

source_name: pooled primary keratinocyte cultures


title: CBS7229

description: Single isolate vs. pooled isolates.

source_name: C. gattii CBS7229 grown in J774 macrophages for 24hrs


title: inVivo_42_b


title: Heat shocked and IPTG induced, replicate #1

city: Clemson

first: Sarah

middle: W

last: Harcum

state: SC

address: 105 Collings Street

department: Bioengineering

institute: Clemson University

description: 34 FI1-2

hyb_protocol: Hybridization of the fragmented cDNA with the Affymetrix Antisense E. coli GeneChip microarrays were conducted according to the manufacturer's instructions.  Briefly, samples were hybridized with the array in a solution containing 100 mM MES buffer, 1 M NaCl, 20 mM EDTA and 0.01% (v/v) Tween 20, pH 6.6 (1X MES).  Additionally, the solution contained 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA and 3.09 μg fragmented-labeled cDNA.  The hybridization cocktail (200 μL) was added to the probe array at room temperature.  The probe array was placed in a rotary hybridization oven set at 60 rpm at 45°C for 16 hours.  Following hybridization, the sample solution was removed and saved.  The probe array was washed and stained automatically by the fluidization station (Affymetrix Inc.) as recommended in the technical manual (Affymetrix, Inc.).  The signals were enhanced with a Streptavidin solution (1X MES stain buffer, 2 mg/mL BSA, 10 μ/ mL streptavidin ).  After the streptavidin solution was removed, an antibody solution (1X MES stain buffer, 2 mg/mL, 0.1 mg/mL normal goat IgG and 5 μg/mL Biotin Anti-streptavidin) was added.  Streptavidin phycoerythrin solution (1X MES stain buffer, 2 mg/mL, 10 μg/mL streptavidin-phycoerythrin) was used to fluorescently label the arrays.

scan_protocol: The wash and stain procedures were carried out by the fluidics station using the ProkGE-fluidics script (Affymetrix Inc.).

data_processing: Microarray suit 5.0 (Affymetrix Inc.) was used to average the scans and process the data, further data analysis was conducted using Affymetrix® Data Mining Tool (DMT 3.0).

source_name: Heat-Shocked, Time 15 min, 5 mM IPTG

label_protocol: The cDNA synthesis was conducted as described in Affymetrix Expression Handbook (Affymetrix Inc., Santa Clara, CA). Briefly, 10 μg of purified total RNA was mixed with 750 ng of random primers (Invitrogen Life Technologies) and incubated at 70°C for 10 minutes.  The samples were cooled to 25°C and incubated for 10 minutes.  RNA/Primer hybridization mixture was mixed with dNTPs (Amersham Pharmacia Biotech), Superscript II reverse transcriptase and 5X 1st Strand Buffer (Invitrogen Life Technologies), SUPERase•ln (Ambion) and DTT.  The cDNA synthesis mixture was incubated at 37°C for 60 minutes, then incubated at 42°C for 60 minutes.  The SuperScript II was heat inactivated by incubation at 70°C for 10 minutes.  The mixture was then cooled to 4°C.  RNA was degraded by the addition of 20 μL 1N NaOH.  The samples were incubated at 65°C for 30 minutes and then neutralized by 20 μL 1N HCl.  The cDNA was purified using QIAquick Columns (QIAquick® Spin Kit, QIAGEN).  cDNA product was eluted with 60 μL of elution buffer supplied with the QIAquick Kit.  Purified cDNA product was quantified by absorbance at 260 nm.  Typical yields were 4-7 μg cDNA.  Four micrograms of purified cDNA was mixed with DNase I and 10X One-phore-All Buffer (Amersham Pharmacia Biotech).  The mixture was incubated at 37°C for 10 minutes followed by inactivation of the DNase I at 98°C for 10 minutes.  Fragmentation was confirmed by separation of the cDNA on 4-20% acrylamide gels (BioRad) stained with SYBR Gold (Molecular Probes).  The majority of the DNA fragments after fragmentation were between 50-200 bases.  The fragmented cDNA was 3′-end-labeled using the Enzo® BioArrayTM Terminal Labeling Kit (Affymetrix Inc., Santa Clara, CA).  Briefly, 5X reaction buffer, 10X CoCl2, 100X Biotin-ddUTP and 50X terminal deoxynucleotides transferase were mixed and incubated at 37°C for 60 minutes.  The reaction was stopped by the addition of 2 μL 0.5 EDTA.  The product was stored at -20°C until the hybridization step.

growth_protocol: The strain MG1655 [pPROEx-CAT] was cultured in a fed-batch fermenter in LB media w/ glucose and a glucose/MgS04 feed at 37 degrees.  Cultures were synchronized to the late log phase, approximately 4.5 hours of fermentation time.

extract_protocol: Fifteen mL fermentation broth was used for each RNA extraction. Harvested cells were rapidly cooled in a -80°C ethanol bath, then centrifuged at 5000 g for seven minutes at 4°C. The supernatant was discarded. The cell pellet was frozen at -80°C. Thawed (on ice) cell pellets were suspended in 150 mL of TE buffer (10 mM Tris-HCl, pH 7.6, 0.1 mM EDTA) containing 0.75 mg/mL lysozyme, and incubated for 15 minutes at room temperature. Total RNA was isolated using RNAqueousTM-Midi Kit (Ambion). The concentration of purified total RNA was determined spectrophotometrically by measuring absorbance at 260 nm. The quality and integrity of the isolated RNA was confirmed by agarose gels (clear 23S and 16S rRNA bands).

treatment_protocol: Cultures were heat-shocked for 15 mins at 50°C at the beginning of the late log phase (~10 OD, 5.0 g dry cell weight).  One set of fermentations were exposed to 5 mM IPTG and one set was not exposed to IPTG.  IPTG was added 8 mins into the heat-shock.  Samples were taken 15 mins after the beginning of the heat-shock.

tag: plasmid

value: pPROEx-CAT


title: Heat shocked and IPTG induced, replicate #2

description: 35 FI2-2


title: Heat shocked and IPTG induced, replicate #3

description: 36 FI2-2


title: Direct_C70 vs C1_1h_3000209701_L

value: vegetative cells grown for 6.5 h in normoxia (70%sat. O2 in air) and then submitted to 1-hour hypoxia (1%sat. O2 in air)


title: Heat shocked, replicate #2

description: 32 FG1-2

source_name: Heat-Shocked, Time 15 min, no IPTG


title: Serine Hydroxamate stressed, replicate #3

description: 39 FK2-2

source_name: E. coli, 1-h, serine hydroxamate

growth_protocol: The strain Escherichia coli MG1655 [pPROEx-CAT] was cultured in a fed-batch fermenter in LB media w/ glucose and a glucose/MgS04 feed at 37 degrees.  Cultures were synchronized to the late log phase, approximately 4.5 hours of fermentation time.  Serine hydrxamate (100mg/L final concentration) was added to the cultures. Samples were taken 1 hour after the beginning the serine hydrxamate addition.

treatment_protocol: Serine hydrxamate (100 mg/L final concentration) was added to the cultures in the late-exponential phase at ~11 OD (~5.5 g g dry cell weight per liter).  Samples for DNA microarray analysis were taken 1 hour after the beginning the serine hydrxamate addition (13.2 OD, ~6.6 g dry cell weight per liter, growth rate 0.15 1/h).


title: Serine Hydroxamate stressed, replicate #2

description: 38 FK2-2


title: Heat shocked, replicate #3

description: 33 FG1-2


title: Cells_newborn_4

tag: tissue


title: inVivo_42_a


title: Cells_newborn_3


title: Serine Hydroxamate stressed, replicate #1

description: 37 FK1-2


title: Wild-type, high cell density, Time S4, IPTG, 3

description: 30 FE2-5

source_name: Wild-Type, high cell density, Time 4 h, 5 mM IPTG

growth_protocol: The strain MG1655 [pPROEx-CAT] was cultured in a fed-batch fermenter in LB media w/ glucose and a glucose/MgS04 feed at 37 degrees.  Cultures were synchronized to the late log phase, approximately 4.5 hours of fermentation time. One set of fermentations were exposed to IPTG and one set was not exposed to IPTG.  Samples were taken 0, 1, and 4 hours post-synchronization (Time S0, S1, and S4).

treatment_protocol: One set of fermentations were exposed to 5 mM IPTG and one set was not exposed to IPTG.  Samples were taken 0, 1, and 4 hours post-synchronization (Time S0, S1, and S4).


title: Wild-type, high cell density, Time S1, IPTG, 3

description: 27 FE2-2

source_name: Wild-Type, high cell density, Time 1 h, 5 mM IPTG


title: inVivo_56_a


title: Wild-type, high cell density, Time S4, IPTG, 2

description: 29 FE2-5


title: inVivo_56_b


title: cells_newborn_1


title: inVivo_28_c


title: Heat shocked, replicate #1

description: 31 FF2-2


title: Wild-type, high cell density, Time S4, IPTG, 1

description: 28 FE1-5


title: Wild-type, high cell density, Time S1, IPTG, 2

description: 26 FE2-2


title: Wild-type, high cell density, Time S4, no IPTG, 3

description: 24 FC2-5

source_name: Wild-Type, high cell density, Time 4 h, no IPTG


title: Wild-type, high cell density, Time S1, IPTG, 1

description: 25 FE1-2


title: inVivo_28_b


title: inVivo_28_a


title: Cells_newborn_2


title: Wild-type, high cell density, Time S4, no IPTG, 1

description: 22 FC1-5


title: Wild-type, high cell density, Time S1, no IPTG, 1

description: 19 FC1-2

source_name: Wild-Type, high cell density, Time 1 h, no IPTG


title: Wild-type, high cell density, Time S1, no IPTG, 2

description: 20 FC2-2


title: Wild-type, high cell density, Time S1, no IPTG, 3

description: 21 FC2-2


title: Wild-type, high cell density, Time S0, no IPTG, 3

description: 18 FC2-1

source_name: Wild-Type, high cell density, Time 0, no IPTG


title: Wild-type, high cell density, Time S4, no IPTG, 2

description: 23 FC2-5


title: inVivo_14_b


title: Wild-type, high cell density, Time S0, no IPTG, 1

description: 16 FC1-1


title: Recombinant, high cell density, Time S4, IPTG, 1

description: 13 FB1-5

source_name: Recombinant, high cell density, Time 4 h, 5 mM IPTG


title: inVivo_14_a


title: Recombinant, high cell density, Time S4, IPTG, 2

description: 14 FB2-5


title: Wild-type, high cell density, Time S0, no IPTG, 2

description: 17 FC2-1


title: Recombinant, high cell density, Time S4, no IPTG, 3

description: 9 FA2-5

source_name: Recombinant, high cell density, Time 4 h, no IPTG


title: Recombinant, high cell density, Time S4, no IPTG, 2

description: 8 FA2-5


title: inVivo_14_c


title: Recombinant, high cell density, Time S1, IPTG, 1

description: 10 FB1-2

source_name: Recombinant, high cell density, Time 1 h, 5 mM IPTG


title: Recombinant, high cell density, Time S1, IPTG, 3

description: 12 FB2-2


title: inVivo_3_b


title: inVivo_3_c


title: Recombinant, high cell density, Time S4, IPTG, 3

description: 15 FB2-5


title: inVivo_3_a


title: Recombinant, high cell density, Time S1, no IPTG, 3

description: 6 FA2-2

source_name: Recombinant, high cell density, Time 1 h, no IPTG


title: CBS1930

description: Single isolate vs. pooled isolates.

source_name: C. gattii CBS1930 grown in J774 macrophages for 24hrs

source_name: Pooled RNA, using equal quantities from each of the 23 samples


title: inVivo_7_d


title: inVivo_7_e


title: Recombinant, high cell density, Time S1, no IPTG, 2

description: 5 FA2-2


title: Recombinant, high cell density, Time S1, IPTG, 2

description: 11 FB2-2


title: Recombinant, high cell density, Time S1, no IPTG, 1

description: 4 FA1-2


title: TGF-β1 treated cells_biological rep 1

first: Victor

middle: John

last: Thannickal

state: AL

address: 1530 3rd Avenue South, THT 422

department: Medicine

institute: University of Alabama at Birmingham

description: Gene expression data from cells treated with TGF-β1

hyb_protocol: Standard Affymetrix protocol.  Affymetrix U133A chips with 22976 probepairs.

scan_protocol: Standard Affymetrix protocol.  GeneChips were scanned using a GeneArray Scanner.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Authors were unable to retrieve CEL files.

source_name: IMR90 cells; TGF-β1 treated

label_protocol: Standard Affymetrix protocol.

growth_protocol: We obtained human fetal lung mesenchymal cells (hFLMCs; IMR-90 cells) from Coriell Cell Repositories, Institute for Medical Research, Camden, NJ.  Cells were cultured in DMEM Life Technologies, Inc.) supplemented with 10% fetal calf serum (Hyclone Laboratories, Logan, UT), 100 U/ml penicillin, 100 μg/ml streptomycin, and 1.25 μg/ml amphotericin B, and incubated  at 37°C in 5% CO2, 95% air.

extract_protocol: Total RNA was isolated from cells using the RNeasy® Mini Kit (Qiagen)

treatment_protocol: Cells were treated with or without TGF-β1 (2ng/ml) and cultured for 18 hours and RNA was isolated from all treatment groups.

tag: cell line

value: IMR90 fetal lung mesenchymal cells

tag: agent


title: TGF-β1 treated cells_biological rep 3


title: Control_no treatment_biological rep 3

description: Gene expression data from untreated cells

source_name: IMR90 cells; no treatment

value: control


title: Recombinant, high cell density, Time S4, no IPTG, 1

description: 7 FA1-5

tag: strain


title: TGF-β1 treated cells_biological rep 2


title: Recombinant, high cell density, Time S0, no IPTG, 3

description: 3 FG1-1

source_name: Recombinant, high cell density, Time 0, no IPTG


title: Control_no treatment_biological rep 2


title: inVitro_7_h


title: inVivo_7_a


title: inVitro_7_f


title: Control_no treatment_biological rep 1


title: inVitro_14_g


title: inVitro_14_j


title: Recombinant, high cell density, Time S0, no IPTG, 2

description: 2 FB1-1


title: Recombinant, high cell density, Time S0, no IPTG, 1

description: 1 FA1-1


title: inVitro_7_i


title: ACC_rep4

status: Public on Aug 06 2009

city: Budapest

first: Viola

last: Tamasi

address: Nagyvarad sqr 4

department: Genetic, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

scan_protocol: Agilent Technologies Scanner G2505B US22502634

data_processing: Agilent Feature Extraction Software. Values are the log 10 rProcessedSignal/gProcessedSignal.

source_name: Adrenocortical carcinoma

label_protocol: ULS labeling (Agilent protocol for 105 K arrays, version 2.0, February 2008)

tag: gender

value: female

tag: age at the time of surgery

value: 61.5 years

value: adrenocortical cancer

tag: status

value: hormonally active

source_name: Control DNA

value: Genomic DNA - Promega G1521


title: CPA_rep3

hyb_protocol: Agilent protocol for 105 K arrays, version 2.0, February 2008

source_name: Adrenocortical adenoma

value: 24.3 years

value: adrenocortical adenoma

value: cortisol producing, hormonally active


title: CPA_rep1

extract_protocol: Agilent protocol for 105 K arrays, version 2.0, February 2008

value: 31.7 years


title: ACC_rep2

value: 48.7 years


title: ACC_rep1

value: 70.4 years


title: V. riparia (VR, PI588259) SD, 13h 28 days - rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007; V. riparia on 3/26/2007) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N).  When vines reached 12-15 nodes (4/25/2007) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h).  Five days after this (4/30/2007) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued.  SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems).  At 1, 3, 7, 14, 21, 28 and 42 days of additional LD or SD, buds were harvested from nodes 3 to 12 from shoot base, immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction.  Three replications (5 vines/replication) were harvested between 05/07-06/07.   After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy.  The endodormant vines were identified after 28 days and moved to cold storage.  The nondormant vines were allowed to grow again and induced into dormancy at a later date.

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Vitis riparia

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Short photoperiod (SD, 13h) 28 days)

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  Three to four shoots were trained vertically on spur pruned greenhouse grown vines.  Vines were watered two times daily at 8:30 am and 3:00 pm.  Environmental Conditions:  Vines were grown in greenhouse at 44N latitude for 30 days LD (15H) then received SD treatment (28 days at 13h).  Daylight was supplemented with HID lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.

extract_protocol: Modified Pine Buffer RNA Extraction Procedure

tag: germplasm name

value: Vitis riparia pi588259

tag: organism part

value: ud:0000001 second order axillary bud

value: UD:0000001 second order axillary bud

tag: development stage

value: UD:0000003 endodormancy

value: 58 days after bud break

tag: growth media

value: peat/perlite/soil


title: IA_rep2

value: female

value: 50.8 years

value: hormonally inactive


title: IA_rep3

value: 45.9 years


title: CPA_rep2

value: 46.8 years

value: Genomic DNA - Promega G1521


title: V. riparia (VR, PI588259) SD, 13h 28 days - rep1

tag: cell type


title: V. riparia (VR, PI588259) SD, 13h 42 days - rep2

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Short photoperiod (SD, 13h) 42 days)

growth_protocol: Growth Description:  Three to four shoots were trained vertically on spur pruned greenhouse grown vines.  Vines were watered two times daily at 8:30 am and 3:00 pm.  Environmental Conditions:  Vines were grown in greenhouse at 44N latitude for 30 days LD (15H) then received SD treatment (42 days at 13h).  Daylight was supplemented with HID lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.

tag: age

value: 72 days after bud break


title: V. riparia (VR, PI588259) SD, 13h 14 days - rep1

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Short photoperiod (SD, 13h) 14 days)

growth_protocol: Growth Description:  Three to four shoots were trained vertically on spur pruned greenhouse grown vines.  Vines were watered two times daily at 8:30 am and 3:00 pm.  Environmental Conditions:  Vines were grown in greenhouse at 44N latitude for 30 days LD (15H) then received SD treatment (14 days at 13h).  Daylight was supplemented with HID lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.

value: 44 days after bud break


title: V. riparia (VR, PI588259) SD, 13h 7 days - rep2

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Short photoperiod (SD, 13h) 7 days)

growth_protocol: Growth Description:  Three to four shoots were trained vertically on spur pruned greenhouse grown vines.  Vines were watered two times daily at 8:30 am and 3:00 pm.  Environmental Conditions:  Vines were grown in greenhouse at 44N latitude for 30 days LD (15H) then received SD treatment (7days at 13h).  Daylight was supplemented with HID lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.

value: 37 days after bud break


title: IA_rep4

value: 61.2 years

value: adrenocortical adenoma

tag: source


title: V. riparia (VR, PI588259) SD, 13h 21 days - rep2

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Short photoperiod (SD, 13h) 21 days)

growth_protocol: Growth Description:  Three to four shoots were trained vertically on spur pruned greenhouse grown vines.  Vines were watered two times daily at 8:30 am and 3:00 pm.  Environmental Conditions:  Vines were grown in greenhouse at 44N latitude for 30 days LD (15H) then received SD treatment (21 days at 13h).  Daylight was supplemented with HID lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.

value: Vitis riparia pi588259

value: 51 days after bud break


title: V. riparia (VR, PI588259) SD, 13h 42 days - rep3

value: ud:0000001 second order axillary bud

value: UD:0000001 second order axillary bud


title: V. riparia (VR, PI588259) SD, 13h 42 days - rep1

value: UD:0000003 endodormancy


title: V. riparia (VR, PI588259) SD, 13h 7 days - rep3

value: peat/perlite/soil


title: V. riparia (VR, PI588259) SD, 13h 3 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Short photoperiod (SD, 13h) 3 days)

growth_protocol: Growth Description:  Three to four shoots were trained vertically on spur pruned greenhouse grown vines.  Vines were watered two times daily at 8:30 am and 3:00 pm.  Environmental Conditions:  Vines were grown in greenhouse at 44N latitude for 30 days LD (15H) then received SD treatment (3 days at 13h).  Daylight was supplemented with HID lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.

value: 33 days after bud break


title: V. riparia (VR, PI588259) SD, 13h 28 days - rep3

value: 58 days after bud break


title: V. riparia (VR, PI588259) SD, 13h 21 days - rep3


title: IA_rep1

value: female

value: 45.5 years

value: hormonally inactive


title: V. riparia (VR, PI588259) SD, 13h 14 days - rep2


title: V. riparia (VR, PI588259) SD, 13h 3 days - rep2


title: V. riparia (VR, PI588259) SD, 13h 1 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Short photoperiod (SD, 13h) 1 days)

growth_protocol: Growth Description:  Three to four shoots were trained vertically on spur pruned greenhouse grown vines.  Vines were watered two times daily at 8:30 am and 3:00 pm.  Environmental Conditions:  Vines were grown in greenhouse at 44N latitude for 30 days LD (15H) then received SD treatment (1 day at  13h).  Daylight was supplemented with HID lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.

value: 31days after bud break


title: V. riparia (VR, PI588259) SD, 13h 14 days - rep3


title: V. riparia (VR, PI588259) SD, 13h 7 days - rep1


title: inVitro_14_k

value: cultured skin substitute

tag: incubation

value: in vitro


title: V. riparia (VR, PI588259) SD, 13h 21 days - rep1


title: ACC_rep3

value: 61.4 years

value: adrenocortical cancer

value: hormonally active

value: Genomic DNA - Promega G1521


title: V. riparia (VR, PI588259) LD, 15h 42 days - rep1

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Long photoperiod (LD, 15h) 42 days)

growth_protocol: Growth Description:  Three to four shoots were trained vertically on spur pruned greenhouse grown vines.  Vines were watered two times daily at 8:30 am and 3:00 pm.  Environmental Conditions:  Vines were grown in greenhouse at 44N latitude with 15h day using supplemental lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.

value: Vitis riparia pi588259

value: UD:0000002 paradormancy

value: 72 days after bud break


title: V. riparia (VR, PI588259) SD, 13h 3 days - rep1

value: ud:0000001 second order axillary bud

value: UD:0000001 second order axillary bud

value: UD:0000003 endodormancy


title: V. riparia (VR, PI588259) SD, 13h 1 days - rep2

growth_protocol: Growth Description:  Three to four shoots were trained vertically on spur pruned greenhouse grown vines.  Vines were watered two times daily at 8:30 am and 3:00 pm.  Environmental Conditions:  Vines were grown in greenhouse at 44N latitude for 30 days LD (15H) then received SD treatment (1 day at 13h).  Daylight was supplemented with HID lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.

value: peat/perlite/soil


title: V. riparia (VR, PI588259) LD, 15h 42 days - rep2


title: V. riparia (VR, PI588259) LD, 15h 28 days - rep1

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Long photoperiod (LD, 15h) 28 days)

value: 58 days after bud break


title: V. riparia (VR, PI588259) LD, 15h 21 days - rep2

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Long photoperiod (LD, 15h) 21 days)

value: 51 days after bud break


title: V. riparia (VR, PI588259) SD, 13h 1 days - rep1


title: V. riparia (VR, PI588259) LD, 15h 28 days - rep3


title: V. riparia (VR, PI588259) LD, 15h 21 days - rep1


title: V. riparia (VR, PI588259) LD, 15h 28 days - rep2


title: V. riparia (VR, PI588259) LD, 15h 14 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Long photoperiod (LD, 15h) 14 days)

value: 44 days after bud break


title: V. riparia (VR, PI588259) LD, 15h 21 days - rep3


title: V. riparia (VR, PI588259) LD, 15h 42 days - rep3


title: V. riparia (VR, PI588259) LD, 15h 14 days - rep2


title: V. riparia (VR, PI588259) LD, 15h 7 days - rep3

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007; V. riparia on 3/26/2007) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N).  When vines reached 12-15 nodes (4/25/2007) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h).  Five days after this (4/30/2007) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued.  SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems).  At 1, 3, 7, 14, 21, 28 and 42 days of additional LD or SD, buds were harvested from nodes 3 to 12 from shoot base, immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction.  Three replications (5 vines/replication) were harvested between 05/07-06/07.   After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy.  The endodormant vines were identified after 28 days and moved to cold storage.  The nondormant vines were allowed to grow again and induced into dormancy at a later date. Three days before harvest of 7 LD samples a violent thunderstorm turned on the automatic irrigation system and LD plants received 10 hours of irrigation.

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Long photoperiod (LD, 15h) 7 days)

value: 37 days after bud break


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 28 days - rep3

organism: Vitis hybrid cultivar

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Short photoperiod (SD, 13h) 28 days)

value: seyval (seyve-villard 5-276)


title: V. riparia (VR, PI588259) LD, 15h 3 days - rep1

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Long photoperiod (LD, 15h) 3 days)

value: 33 days after bud break


title: V. riparia (VR, PI588259) LD, 15h 7 days - rep2


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 42 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Short photoperiod (SD, 13h) 42 days)


title: V. riparia (VR, PI588259) LD, 15h 3 days - rep3


title: V. riparia (VR, PI588259) LD, 15h 14 days - rep1


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 42 days - rep1


title: V. riparia (VR, PI588259) LD, 15h 1 days - rep3

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) Long photoperiod (LD, 15h) 1 days)

value: 31 days after bud break


title: V. riparia (VR, PI588259) LD, 15h 7 days - rep1

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007; V. riparia on 3/26/2007) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N).  When vines reached 12-15 nodes (4/25/2007) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h).  Five days after this (4/30/2007) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued.  SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems).  At 1, 3, 7, 14, 21, 28 and 42 days of additional LD or SD, buds were harvested from nodes 3 to 12 from shoot base, immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction.  Three replications (5 vines/replication) were harvested between 05/07-06/07.   After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy.  The endodormant vines were identified after 28 days and moved to cold storage.  The nondormant vines were allowed to grow again and induced into dormancy at a later date.  Three days before harvest of 7 LD samples a violent thunderstorm turned on the automatic irrigation system and LD plants received 10 hours of irrigation.


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 42 days - rep2


title: V. riparia (VR, PI588259) LD, 15h 1 days - rep2


title: V. riparia (VR, PI588259) LD, 15h 1 days - rep1


title: V. riparia (VR, PI588259) LD, 15h 3 days - rep2


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 28 days - rep2


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 28 days - rep1


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 21 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Short photoperiod (SD, 13h) 21 days)


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 21 days - rep1


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 3 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Short photoperiod (SD, 13h) 3 days)


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 14 days - rep1

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Short photoperiod (SD, 13h) 14 days)


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 14 days - rep3


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 14 days - rep2


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 3 days - rep1


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 7 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Short photoperiod (SD, 13h) 7 days)

growth_protocol: Growth Description:  Three to four shoots were trained vertically on spur pruned greenhouse grown vines.  Vines were watered two times daily at 8:30 am and 3:00 pm.  Environmental Conditions:  Vines were grown in greenhouse at 44N latitude for 30 days LD (15H) then received SD treatment (7 days at 13h).  Daylight was supplemented with HID lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 21 days - rep2


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 7 days - rep1


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 7 days - rep2


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 3 days - rep2


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 1 days - rep2

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Short photoperiod (SD, 13h) 1 days)


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 1 days - rep1


title: Seyval (SV, Seyve Villard 5-276) SD, 13h 1 days - rep3


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 28 days - rep2

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Long photoperiod (LD, 15h) 28 days)


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 42 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Long photoperiod (LD, 15h) 42 days)


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 28 days - rep1


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 21 days - rep2

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Long photoperiod (LD, 15h) 21 days)


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 21 days - rep3


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 42 days - rep2


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 21 days - rep1


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 14 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Long photoperiod (LD, 15h) 14 days)


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 3 days - rep1

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Long photoperiod (LD, 15h) 3 days)


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 14 days - rep2


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 42 days - rep1


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 3 days - rep3


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 7 days - rep3

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Long photoperiod (LD, 15h) 7 days)


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 28 days - rep3


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 7 days - rep2


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 7 days - rep1


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 14 days - rep1


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 1 days - rep2

source_name: second order axillary bud (genotype: Seyval (SV, Seyve Villard 5-276) Long photoperiod (LD, 15h) 1 days)


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 3 days - rep2


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 1 days - rep3

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007; V. riparia on 3/26/2007) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N).  When vines reached 12-15 nodes (4/25/2007) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h).  Five days after this (4/30/2007) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued.  SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems).  At 1, 3, 7, 14, 21, 28 and 42 days of additional LD or SD, buds were harvested from nodes 3 to 12 from shoot base, immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction.  Three replications (5 vines/replication) were harvested between 05/07-06/07.   After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy.  The endodormant vines were identified after 28 days and moved to cold storage.  The nondormant vines were allowed to grow again and induced into dormancy at a later date.ere allowed to grow again and induced into dormancy at a later date.


title: Global gene expression of NASH patients, Normal control A249

city: Buffalo

first: Susan

last: Baker

address: 3435 Main street, 422 BRB

department: Pediatrics

institute: SUNY at Buffalo

description: These samples were derived from liver grafts of normal subjects with normal body mass index. The ages of these normal controls were matched with our NASH patients. No liver diseases were diagnosed with these normal controls. Although the biochemistry data provided by Admet were limited, the healthy status of these livers was ascertained by the lower transcription levels of marker genes for inflammation and fibrosis.

hyb_protocol: 1, Fragmentation of cRNA. 2, Denature cRNA at 90C for 5 min. 3, Hybridization was performed at 37 C, for 18-24 hours. 4, Detection with Cy5-streptavidin conjugate.

scan_protocol: Microarray scanning and data acquisition were done at the gene expression facility, Roswell Park Cancer Institute, following their routine standard procedure.

data_processing: Data were median-normalized for comparison.

source_name: Total RNA purchased from ADMET Technologies (Durham, NC), extracted from healthy liver tissue.

label_protocol:
Complementary DNA was prepared from total RNA.
In vitro transcription was then performed with biotin labeled substrate to produce biotin labeled cRNA.

extract_protocol: Samples were stored in RNAlater at -80 freezer before total RNA extraction with Qiagen RNeasy kit.

tag: disease state

value: normal (control)

value: liver


title: Liver_BXD45_M_B8

city: Chapel Hill

first: Daniel

middle: M

last: Gatti

state: NC

address: 135 Dauer Dr.

department: Environmental Sciences & Engineering

institute: University of Noth Carolina

hyb_protocol: Equal amounts of Cy3 and Cy5 labeled cRNA (750 ng) from the individual animals and from the pooled control, respectively, were hybridized to an Agilent Mouse Oligo Microarray (~21,000 features, catalogue# G4121) for 17 hours at 65°C. The hybridized microarrays were then washed and scanned using an Agilent G2565BA scanner.

scan_protocol: scanned using the Agilent G2565BA scanner

data_processing: Data were extracted from the scanned image using Agilent Feature Extraction software version 6.1. A total of 122 arrays were run in 8 batches. The samples were semirandomly distributed throughout the batches prior to microarray analysis in order to separate sexes and strains, and to minimize between- and within- batch bias. Technical and biological replicates were run both within each batch and between batches. The microarray data was deposited in the UNC Microarray Database and extracted using Log2 ratios of the mean red channel intensity over the mean green channel intensity. This was followed by LOWESS normalization to remove the intensity dependent dye bias3. Neither the genes nor the arrays were centered. Inter-batch normalization was carried out using a nested ANOVA mixed model with samples within each batch crossed with sex and strain.

source_name: Liver

label_protocol: A balanced design was used to assign samples across 8 microarray batches. Each batch was balanced by sex and strain and contained both inter and intrabatch technical replicates. The randomized batch design of the microarray experiment minimizes the effect of interbatch variance. Further, the pooling of mRNA from multiple mice within strain/sex reduces the effects of individual variation in the measurement of transcript expression. One μg of total RNA from 3 individual mouse liver samples of the same sex and strain was pooled, amplified and labeled with a fluorescent dye (Cy5) and a common reference - pooled mouse tissues (equal amounts of RNA from liver, kidney, lung, brain and spleen) mRNA isolated from the livers of 100 male C57BL6/J mice [see2 for details] - were amplified and labeled with Cy3 using Agilent Technologies (Palo Alto, CA) Low RNA Input Linear Amplification labeling kit following the manufacturer’s protocol. The quantity of the resulting fluorescently labeled cRNA was measured using a Nanodrop ND-100 spectrophometer (Nanodrop Technologies, Wilmington, DE) and its integrity assessed using an Agilent Bioanalyzer.

growth_protocol: Animals and Tissues. BXD1 through BXD42 mice are original RI strains available from the Jackson Laboratory (Bar Harbor, ME). BXD43 through BXD100 lines were generated using ninth or tenth generation Advanced Intercross Line (AIL) progenitors. AILs are generated by breeding two inbred parents (here is C57BL/6J and DBA/2J) and crossing their offspring so as to minimize inbreeding and maximize recombination events at each generation1. Great care was taken to minimize the effects of gene-environment interactions. Mice were maintained under identical conditions with respect to diet, water and housing conditions. Mice were maintained at 20-24°C on a 14/10 hr light/dark cycle in a pathogen-free colony at the University of Tennessee-Memphis. Animals were fed a 5% fat Agway Prolab 3000 rat and mouse chow and given tap water in glass bottles. Mice were raised to between 54 and 177 days (mean 70 days) of age. Liver tissues were collected following sacrifice by cervical dislocation. The whole liver was removed immediately, and placed in five volumes of RNAlater (Ambion, Austin, TX) at 4°C overnight, before removing from RNAlater and storing at -80°C until processing. All animal studies for this project were approved by Animal Care and Use Committee at the University of Tennessee-Memphis.

extract_protocol: RNA Isolation. Total RNA was isolated from liver samples (~30 mg) using the Rneasy mini kit (Qiagen, Valencia, CA) as detailed by the manufacturer. RNA quality and quantity was determined spectrophotometrically from the absorbance at 260 nm and 280 nm. Aliquots of RNA samples were frozen at −80°C until microarray analysis. For each microarray, RNA was pooled from 2-3 mice of the same sex and strain. All strains used one array per sex per strain except for strains 23, 34 and 33. The proportion of males to female is approximately equal.

value: M

tag: batch

value: Liver

source_name: Pooled Reference

tag: sample

value: pooled RNA from the same batch


title: Liver_BXD48_F_B8

value: F

tag: tissue


title: Liver_BXD51_F_B8


title: Liver_BXD92_M_B8


title: Liver_BXD85_M_B8


title: Global gene expression of NASH patients, Normal control A138


title: Liver_BXD73_F_B8


title: Liver_BXD11TY_F_B8


title: Liver_BXD39_F_B8


title: Liver_BXD36_F_B8


title: Seyval (SV, Seyve Villard 5-276) LD, 15h 1 days - rep1

value: ud:0000001 second order axillary bud

value: UD:0000002 paradormancy


title: Liver_BXD86_M_B8


title: Liver_DBA2J_F_B8


title: Liver_BXD2_M_B8


title: Liver_BXD69_M_B8


title: Liver_BXD33_F_B8


title: Liver_BXD19_M_B8


title: Liver_BXD5_M_B7


title: Liver_BXD42_F_B7


title: Liver_BXD14_F_B8


title: Liver_BXD6_F_B7


title: Liver_BXD43_M_B7


title: Liver_C57BL6J_F_B8_rep2


title: Liver_BXD38_M_B7


title: Liver_B6D2F1_F_B8


title: Liver_BXD29_M_B7


title: Liver_BXD16_F_B8


title: Liver_DBA2J_F_B7


title: Liver_C57BL6J_F_B8_rep1


title: Liver_DBA2J_M_B7


title: Liver_C57BL6J_F_B7_rep2


title: Liver_C57BL6J_F_B7_rep1


title: Liver_BXD2_F_B6


title: Liver_BXD48_M_B6


title: Liver_BXD33_F_B6


title: Liver_BXD21_F_B6


title: Liver_BXD44_M_B6


title: Liver_BXD34_M_B6


title: Liver_BXD24_M_B6


title: Liver_BXD9_M_B6


title: Liver_BXD77_F_B5


title: Liver_DBA2J_M_B6


title: Liver_BXD28_F_B5


title: Liver_C57BL6J_F_B6_rep1


title: Liver_C57BL6J_M_B6


title: Liver_DBA2J_F_B6


title: Liver_BXD45_F_B5


title: Liver_BXD31_F_B6


title: Liver_BXD12_M_B5


title: Liver_C57BL6J_F_B5_rep2


title: Liver_C57BL6J_F_B6_rep2


title: Liver_BXD60_F_B5


title: Liver_BXD1_F_B5


title: Liver_DBA2J_F_B5


title: Liver_BXD51_M_B4R


title: Liver_BXD13_M_B5


title: Liver_BXD85_F_B4R


title: Liver_BXD62_F_B4R


title: Liver_C57BL6J_F_B5_rep1


title: Liver_BXD15_M_B5


title: Liver_BXD73_M_B4R


title: Liver_BXD92_F_B4R


title: Liver_BXD8_M_B4R


title: Liver_BXD86_F_B4R


title: Liver_BXD19_F_B4R


title: Liver_BXD40_M_B4R


title: Liver_BXD69_F_B4R


title: Liver_BXD16_M_B4R


title: Liver_BXD23_F_B4R


title: Liver_BXD24_F_B4R


title: Liver_B6D2F1_F_B3


title: Liver_BXD32_M_B4R


title: Liver_DBA2J_F_B4R_rep2


title: Liver_BXD6_M_B3


title: Liver_DBA2J_F_B4R_rep1


title: Liver_DBA2J_M_B3


title: Liver_BXD60_M_B3


title: Liver_BXD36_M_B3


title: Liver_C57BL6J_F_B3_rep2


title: Liver_C57BL6J_F_B4R_rep2


title: Liver_C57BL6J_F_B4R_rep1


title: Liver_C57BL6J_F_B4R


title: Liver_BXD15_F_B3


title: Liver_BXD9_F_B3


title: Liver_DBA2J_F_B3


title: Liver_BXD38_F_B3


title: Liver_BXD14_M_B3


title: Liver_C57BL6J_F_B3_rep1


title: Liver_C57BL6J_M_B3_rep2


title: Liver_C57BL6J_M_B3_rep1


title: Liver_B6D2F1_M_B3


title: Liver_BXD44_F_B3


title: Liver_BXD62_M_B2


title: HUVEC_Vector_4OHT

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

hyb_protocol: Following fragmentation, 15mg of cRNA were hybridized for 16hr on Affymetrix GeneChip HG-U133 Plus 2 (whole genome) as recommended by manufacturer

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data were analyzed with PLIER using Array assist 6.5 and GeneSpring GX10 software

source_name: Human Umbilical Vein Endothelial Cells

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer’s instructions

growth_protocol: HUVECs were grown in EMB medium containing 10% FBS (fetal bovine serum)  supplemented with the bullet kit. Cells were used for experiments at passages 2 to 6. HUVECs stably transduced with either a MSCVneo vector or MSCVneo expressing a 4-Hydroxytamoxifen (4-OHT)-inducible K13-ERTAM.

extract_protocol: RNA was extracted from the cells using  RNeasy mini kit (Qiagen Valenica, CA)

treatment_protocol: Cells were grown in presence or absence of 4OHT.

value: Human Umbilical Vein Endothelial Cells

value: primary cells


title: HUVEC_Vector_UT


title: Liver_BXD43_F_B2


title: HUVEC_K13_ER_4OHT


title: Liver_BXD5_F_B2


title: Liver_BXD32_F_B2


title: Liver_BXD21_M_B2


title: Liver_B6D2F1_F_B2


title: Liver_BXD42_M_B2


title: SW149_6-7

city: Rochester

first: Craig

middle: A.

last: Mullen

address: 601 Elmwood Ave., Box 777

institute: University of Rochester

description: NSTY ALL in allogeneic BMT animal 5

hyb_protocol: Hybridization, washes, and staining with phycoerythrin-streptavidin (including antibody enhancement step) were carried out as recommended by Affymetrix for eukaryotic expression arrays, using hybridization oven and fluidics station purchased from Affymetrix

scan_protocol: Scans were done with Affymetrix scanner exactly as recommended by Affymetrix.

data_processing: Values were generated by default settings in Export Expression Values in dCHIP after reading in CEL data files

source_name: NSTY ALL growing in animal after allogeneic transplant

label_protocol: Biotinylated cDNA was prepared with kits from NuGEN as recommended by supplier

growth_protocol: The bone marrow transplant model involved preparation of C57BL/6 recipients with total body irradiation and 5-fluoruracil. These recipients were then infused IV with either allogeneic C3.SW marrow and spleen cells or syngeneic C57BL/6 marrow and spleen cells. The leukemia cells were mixed in with the marrow and spleen cells.  After a few weeks (2-3) the C57BL/6 leukemia cells were purified by flow cytometry and passed into other freshly transplanted animals. After three serial transplants the leukemia cells were flow purified and RNA prepared.

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

treatment_protocol: Leukemia flow sorted on GFP marker. Immediately then placed in Trizol.

value: flow cytometry sorted leukemia from bone marrow


title: Liver_BXD11_M_B2


title: Liver_B6D2F1_M_B2


title: Liver_BXD31_M_B2


title: Liver_BXD13_F_B2


title: Liver_DBA2J_M_B2


title: SW149_5-7

description: NSTY ALL in allogeneic BMT animal 3


title: SW149_6-3

description: NSTY ALL in allogeneic BMT animal 4


title: SW149_2-3

description: NSTY ALL in allogeneic BMT animal 2


title: SW149_1-3

description: NSTY ALL in allogeneic BMT animal 1


title: Liver_DBA2J_F_B2_rep1


title: B6149_6

description: NSTY ALL in syngeneic BMT animal 4

source_name: NSTY ALL growing in animal after syngeneic transplant


title: B6149_3

description: NSTY ALL in syngeneic BMT animal 2


title: Liver_DBA2J_F_B2_rep2


title: B6149_5

description: NSTY ALL in syngeneic BMT animal 3


title: Liver_BXD8_F_B1


title: Liver_C57BL6J_F_B2


title: B6149_8

description: NSTY ALL in syngeneic BMT animal 5


title: Liver_C57BL6J_M_B2_rep2


title: HUVEC_K13_ER_UT


title: Liver_BXD40_F_B1


title: Mouse fetal liver_E14.5_KO_rep3

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: One fetal liver was used for each replicate

hyb_protocol: 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip Operating Software (Version 1.2.0.037).

data_processing: The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 7.1).  This system performs data pre-processing and error modeling as described in Weng (2006).  Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.

source_name: Embryonic day 14.5 Zfp36l2 knockout (KO) mouse fetal liver

label_protocol: Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix Amplification One-Cycle Target labeling kit according to manufacturer's protocol.

extract_protocol: Qiagen Rneasy protocol using mini columns; elute RNA with 70 degree water

value: Embryonic day 14.5

tag: genotype

value: Zfp36l2 knockout (KO)

tag: tissue type

value: fetal liver

value: b6, 129 mixed background strain


title: B6149_1

description: NSTY ALL in syngeneic BMT animal 1


title: Liver_BXD39_M_B1

tag: strain

tag: gender


title: Mouse fetal liver_E14.5_KO_rep5


title: Liver_BXD12_F_B1


title: Liver_BXD77_M_B1


title: Liver_BXD28_M_B1


title: Liver_BXD34_F_B1


title: Liver_BXD29_F_B1


title: Liver_BXD23_M_B1


title: Mouse fetal liver_E14.5_KO_rep2


title: Mouse fetal liver_E14.5_KO_rep4


title: Mouse fetal liver_E14.5_KO_rep1


title: Liver_B6D2F1_M_B1