title: 150 ppm Zn vs 2000 ppm Zn oligo 1

status: Public on Oct 02 2008

city: East Lansing

first: Catherine

middle: W.

last: Ernst

state: MI

address: 3330 Anthony Hall

department: Animal Science

institute: Michigan State University

description: Oligonucleotide microarrays used for this study consisted of 13,297 70-mer oligos (Pig Array-Ready Oligo Set v. 1.0 and Pig Oligo Extension Set v. 1.0, Qiagen, Inc., Valencia, CA) each spotted once on a single slide.  Slides were printed at the Michigan State University Research Technology Support Facility.  Oligonucleotides spotted in multiple locations for use as potential controls included 76 Arabidopsis thaliana gene spots, 17 beta tubulin spots, 17 glyceraldehyde-3-phosphate dehydrogenase spots, 85 heat shock protein gene spots, 69 ribosomal protein gene spots, 112 randomly generated negative control spots and 470 blanks.

hyb_protocol: The concentrated probe was combined with 100 µl of Slide Hyb#3 solution (Ambion, Inc. Austin, TX) and denatured at 70ºC for 5 min.  Microarray hybridizations took place in sealed hybridization chambers in a GeneTAC™ Hybridization Station (Genomic Solutions) for 18 hours using step-down temperatures ranging from 65ºC to 42ºC.  Following hybridization, the slides were washed twice with medium stringency buffer and once with high stringency buffer (Genomic Solutions).  The slides were rinsed in 2XSSC and deionized water and were dried using centrifugation at 1000xg for 2 min.

scan_protocol: Fluorescent images were detected on a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).  Fluorescence intensity data were collected using GenePix software (Molecular Devices) after spot alignment.

data_processing: Log ratio of Loess Normalized Cy3 versus Cy5.

organism: Sus scrofa

source_name: 150ppm Zn A1

label_protocol: For each sample, 8 µg of total RNA was reverse transcribed with an oligo dt18 primer using the Superscript Indirect cDNA Labeling System (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.  After first-strand synthesis and purification, the cDNAs incorporated amino-modified dUTPs and were labeled with N-hydroxysuccinate (NHS) ester Cy3 or Cy5 dyes (GE Healthcare, Piscataway, NJ).  The labeled cDNAs were purified, combined and concentrated to 10 µl using a microcon spin column (Millipore, Bedford, MA).

extract_protocol: Liver tissue was taken from newly weaned pigs fed dietary Zn as Zn oxide for 14 days at either adequate (150 Zn/kg) or pharmacological (2000 mg Zn/kg) levels. Total RNA was isolated from liver tissue using TRIzol Reagent (GIBCO BRL, Life Technologies) according to the manufacturer’s protocol.

tag: Tissue

value: Liver

tag: Diet

value: 150 ppm Zn as Zn oxide

source_name: 2000 ppm Zn E1

value: 2000 ppm Zn as Zn oxide


title: reference decay profile 2, t=0

status: Public on Oct 01 2008

type: RNA

city: Rehovot

first: Ophir

last: Shalem

address: Hertzel

country: Israel

institute: Weizmann Inst.

description: Reference decay profile 2, t=0

data_processing: RMA algorithm followed by normalization using spiked-in RNA as explained in detail in the supplementary of the paper (Shalem et al.).

label: biotin

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: No treatment, time 0 following transcription inhibition

label_protocol: cDNA was prepared using poly(T) primers, labeled cRNA was prepared using the GeneChip system according to manufacturer instructions.

growth_protocol: Yeast strain Y262 (carrying a temperature-sensitive mutation in RNA polymerase II) was grown in YPD to mid-log phase in 26 degrees.

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

treatment_protocol: In the oxidative stress and DNA damage experiments, cells were treated with 0.3mM H2O2 or 0.1% MMS, 25 or 40 minutes prior to transcription inhibition. At time point 0, the temperature of the culture was raised to 37 degrees by adding an equal amount of medium prewarmed to 49 degrees. This step inactivated the temperature-sensitive RNA polymerase II and therefore stopped transcription. Following transcription inhibition, 10 samples were taken for each time course (0,  5 min, 10 min, 15 min, 20 min, 30 min, 40 min, 50 min, 60 min) and a technical replicate of time point zero. In the second reference decay profile, the three last time points (40 min, 50 min, and 60 min) turned out to be outliers, and thus were not used and not submitted.

tag: strain Y262


title: reference decay profile 1, t=5min

description: Reference decay profile 1, t=5 min

hyb_protocol: GeneChip system according to manufacturer instructions.

source_name: No treatment, 5 min following transcription inhibition


title: reference decay profile 2, t=10min

description: Reference decay profile 2, t=10 min

scan_protocol: GeneChip system according to manufacturer instructions.

source_name: No treatment, 10 min following transcription inhibition


title: reference decay profile 1, t=10min

description: Reference decay profile 1, t=10 min


title: 150 ppm Zn vs 2000 ppm Zn oligo 4

country: USA

molecule: total RNA

source_name: 2000 ppm Zn E4

source_name: 150 ppm Zn A4


title: DNA damage decay profile, t=40min

description: Decay profile following DNA damage, t=40 min

source_name: MMS treatment, 40 min following transcription inhibition


title: DNA damage decay profile, t=20min

description: Decay profile following DNA damage, t=20 min

source_name: MMS treatment, 20 min following transcription inhibition


title: DNA damage decay profile, t=30min

description: Decay profile following DNA damage, t=30 min

source_name: MMS treatment, 30 min following transcription inhibition


title: DNA damage decay profile, t=0, replicate

description: Decay profile following DNA damage, t=0

source_name: MMS treatment, time 0 following transcription inhibition


title: DNA damage decay profile, t=15min

description: Decay profile following DNA damage, t=15 imin

source_name: MMS treatment, 15 min following transcription inhibition


title: DNA damage decay profile, t=50min

description: Decay profile following DNA damage, t=50 min

source_name: MMS treatment, 50 min following transcription inhibition


title: DNA damage decay profile, t=10min

description: Decay profile following DNA damage, t=10 min

source_name: MMS treatment, 10 min following transcription inhibition


title: 150 ppm Zn vs 2000 ppm Zn oligo 3

source_name: 2000 ppm Zn E3

source_name: 150 ppm Zn A3


title: oxidative stress decay profile, t=50min

description: Decay profile following oxidative stress, t=50 min

source_name: H2O2 treatment, 50 min following transcription inhibition


title: DNA damage decay profile, t=5min

description: Decay profile following DNA damage, t=5 min

source_name: MMS treatment, 5 min following transcription inhibition


title: DNA damage decay profile, t=0

description: Decay profile following DNA damage, t=0


title: oxidative stress decay profile, t=60min

description: Decay profile following oxidative stress, t=60 min

source_name: H2O2 treatment, 60 min following transcription inhibition


title: oxidative stress decay profile, t=5min

description: Decay profile following oxidative stress, t=5 min

source_name: H2O2 treatment, 5 min following transcription inhibition


title: oxidative stress decay profile, t=10min

description: Decay profile following oxidative stress, t=10 min

source_name: H2O2 treatment, 10 min following transcription inhibition


title: DNA damage stress, t=180min

description: Gene expression following treatment with 0.1% of MMS

data_processing: RMA algorithms using bioconductor software implemented in R.

source_name: 180 min following MMS treatment

growth_protocol: Cells were grown in YPD to mid-log phase in 25 degrees.

treatment_protocol: At time 0, cells were treated with 0.3mM of H2O2 or 0.1% of MMS.


title: oxidative stress decay profile, t=0

description: Decay profile following oxidative stress, t=0

source_name: H2O2 treatment, time 0 following transcription inhibition


title: oxidative stress decay profile, t=0, replicate


title: oxidative stress decay profile, t=15min

description: Decay profile following oxidative stress, t=15 min

source_name: H2O2 treatment, 15 min following transcription inhibition


title: reference decay profile 1, t=15min

description: Reference decay profile 1, t=15 min

source_name: No treatment, 15 min following transcription inhibition


title: reference decay profile 1, t=20min

description: Reference decay profile 1, t=20 min

source_name: No treatment, 20 min following transcription inhibition


title: DNA damage decay profile, t=60min

description: Decay profile following DNA damage, t=60 min

source_name: MMS treatment, 60 min following transcription inhibition


title: reference decay profile 2, t=20min

description: Reference decay profile 2, t=20 min


title: DNA damage stress, t=100min

source_name: 100 min following MMS treatment


title: reference decay profile 2, t=30min

description: Reference decay profile 2, t=30 min

source_name: No treatment, 30 min following transcription inhibition


title: oxidative stress decay profile, t=20min

description: Decay profile following oxidative stress, t=20 min

source_name: H2O2 treatment, 20 min following transcription inhibition


title: DNA damage stress, t=140min

source_name: 140 min following MMS treatment


title: oxidative stress decay profile, t=30min

description: Decay profile following oxidative stress, t=30 min

source_name: H2O2 treatment, 30 min following transcription inhibition


title: oxidative stress decay profile, t=40min

description: Decay profile following oxidative stress, t=40 min

source_name: H2O2 treatment, 40 min following transcription inhibition


title: reference decay profile 1, t=30min

description: Reference decay profile 1, t=30 min


title: DNA damage stress, t=60min

source_name: 60 min following MMS treatment


title: 150 ppm Zn vs 2000 ppm Zn oligo 2

description: Oligonucleotide microarrays used for this study consisted of 13,297 70-mer oligos (Pig Array-Ready Oligo Set v. 1.0 and Pig Oligo Extension Set v. 1.0, Qiagen, Inc., Valencia, CA) each spotted once on a single slide.  Slides were printed at the Michigan State University Research Technology Support Facility.  Oligonucleotides spotted in multiple locations for use as potential controls included 76 Arabidopsis thaliana gene spots, 17 beta tubulin spots, 17 glyceraldehyde-3-phosphate dehydrogenase spots, 85 heat shock protein gene spots, 69 ribosomal protein gene spots, 112 randomly generated negative control spots and 470 blanks.

source_name: 150 ppm Zn A2

source_name: 2000 ppm Zn E2


title: DNA damage stress, t=30min

source_name: 30 min following MMS treatment


title: oxidative stress, t=180min

description: Gene expression following treatment with 0.3mM of H2O2

source_name: 180 min following H2O2 treatment


title: DNA damage stress, t=0

source_name: time 0 following MMS treatment


title: oxidative stress, t=100min

source_name: 100 min following H2O2 treatment


title: oxidative stress, t=140min

source_name: 140 min following H2O2 treatment


title: oxidative stress, t=0

source_name: time 0 following H2O2 treatment


title: oxidative stress, t=30min

source_name: 30 min following H2O2 treatment


title: oxidative stress, t=60min

source_name: 60 min following H2O2 treatment


title: Crown tissue of Solstice at 5 weeks post germination

city: Bristol

first: Mark

middle: Owen

last: Winfield

address: Woodland Road

department: Biological Sciences

country: United Kingdom

institute: Bristol University

description: CONTROL sample to allow separation one to distinguish cold induced responses in gene expression from those that result from a decline in day-length and light.

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

scan_protocol: GeneChip Wheat Genome Arrays wee scanned with the GeneChip 3000.

data_processing: The data were analysed using GeneSpring GX 7.3: raw data was imported from .CEL files and normalised using RMA.  Within GeneSpring GX, per gene normalisation to the median was perfored.

label: Biotin

organism: Triticum aestivum

source_name: Solstice crown 5 weeks post-germination (no vernalisation)

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: Seeds were planted in 50:50 potting compost:perlite in 10 cm pots and maintained in growth cabinets with a 14 h photoperiod (PAR 280) and 16°C day/14°C night.  After three weeks of these conditions, plants were gradually exposed to a decline in temperature, day-length and light intensity: week 3-4 = 14 h photoperiod (PAR 280), 14°C day/12°C night; week 4-5 = 12 h photoperiod (PAR 185), 14°C day/10°C night;week 5--6 = 11 h photoperiod (PAR 185), 12°C day/10°C night;week 6-7 = 11 h photoperiod (PAR 185), 12°C day/8°C night;week 7-8 = 10 h photoperiod (PAR 95), 10°C day/6°C night;week 8-9 = 9 h photoperiod (PAR 95), 8°C day/4°C night;week 9-10 = 8 h photoperiod (PAR 95), 6°C day/2°C night;week 10-11 = 8 h photoperiod (PAR 95), 4°C day/2°C night;week 11-12 = 8 h photoperiod (PAR 48), 2°C day/2°C night.

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

tag: variety

value: Solstice

tag: Grown for three weeks with 14 hour photoperiod; 16°C day 14°C night; PAR = 280 then an additional 2 weeks with declining day-length and light intensity only.


title: Crown tissue of Solstice at 3 weeks post germination

source_name: Solstice crown 3 weeks post-germination

tag: Grown for three weeks with 14 hour photoperiod; 16°C day 14°C night; PAR = 280.


title: Human MCF7stables cells, HAE2F1dbdmut Replicate 2

type: genomic

city: Davis

first: Alina

last: Rabinovich

state: CA

address: 451 Health Science Dr.

department: Genome Center

institute: UC Davis

description: Human MCF7stables cells

hyb_protocol: 12 ug of the Cy5-labeled ChIP sample and 12 ug of the Cy3-labeled total sample were mixed, dried down, and resuspended in 40 μl of NimbleGen Hybridization Buffer (NimbleGen Systems).After denaturation, hybridization was carried out in a MAUI Hybridization System (BioMicro Systems) for 18 h at 42°C. The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems) and dried by centrifugation.

scan_protocol: The arrays were scanned at 5-μm resolution using the GenePix 4000B scanner (Axon Instruments)

data_processing: Fluorescence intensity raw data was obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). For each spot on the array, log2-ratios of the Cy5-labeled test sample versus the Cy3-labeled reference sample were calculated. Then, the biweight mean of this log2 ratio was subtracted from each point; this procedure similar to mean-normalization of each channel

molecule: genomic DNA

organism: Homo sapiens

source_name: MCF7stables cells

label_protocol: DNA sample (1 μg) was denatured in the presence of 5'-Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reaction was terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.

extract_protocol:
ChIP assay was performed following the ChIP protocol provided at http://www.genomecenter.ucdavis.edu/farnham and
http://genomecenter.ucdavis.edu/expression_analysis.

tag: HAE2F1dbdmut antibody

label_protocol: DNA sample (1 μg) was denatured in the presence of 5'-Cy3-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reaction was terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.

tag: control total input


title: Leaf tissue of Solstice at 5 weeks post germination

source_name: Solstice leaf 5 weeks post-germination (no vernalisation)


title: Human MCF7stables cells, HAvector Replicate 2

description: Human MCF7stables cells

tag: HAvector antibody


title: Leaf tissue of Solstice at 9 weeks post germination

source_name: Solstice leaf 9 weeks post-germination (no vernalisation)

tag: Grown for three weeks with 14 hour photoperiod; 16°C day 14°C night; PAR = 280 then an additional 6 weeks with declining day-length and light intensity only.


title: Crown tissue of Solstice at 9 weeks post germination, biological rep 1

description: Plants 9 weeks post-germination; after 3 weeks' growth under standard conditions plants temperature, day-length and light intensity were reduced.

source_name: Solstice crown 9 weeks post-germination (6 weeks vernalisation)

tag: Grown for three weeks with 14 hour photoperiod; 16°C day 14°C night; PAR = 280 then an additional 6 weeks with declining temp, day-length and light intensity.


title: Crown tissue of Solstice at 5 weeks post germination, biological rep 1

description: Plants 5 weeks post-germination; after 3 weeks' growth under standard conditions plants temperature, day-length and light intensity were reduced.

source_name: Solstice crown 5 weeks post-germination (2 weeks vernalisation)

tag: Grown for three weeks with 14 hour photoperiod; 16°C day 14°C night; PAR = 280 then an additional 2 weeks with declining temp, day-length and light intensity.


title: Crown tissue of Solstice at 3 weeks post germination, biological rep 2

description: Plants 3 weeks post-germination treated with standard conditions (14 hour photoperiod; 16°C day 14°C night; PAR = 280).  These are the reference samples for the determination of change in gene expression.


title: Leaf tissue of Solstice at 3 weeks post germination

source_name: Solstice leaf 3 weeks post-germination


title: Crown tissue of Solstice at 9 weeks post germination, biological rep 2


title: Crown tissue of Solstice at 5 weeks post germination, biological rep 2


title: Crown tissue of Solstice at 9 weeks post germination

source_name: Solstice crown 9 weeks post-germination (no vernalisation)


title: Leaf tissue of Solstice at 9 weeks post germination, biological rep 2

source_name: Solstice leaf 9 weeks post-germination (6 weeks vernaluisation)


title: Human MCF7stables cells, HAE2F1wt Replicate 1

description: Human MCF7stables cells

tag: HAE2F1wt antibody


title: Human MCF7stables cells, HAE2F1wt Replicate 2

description: Human MCF7stables cells


title: Crown tissue of Solstice at 3 weeks post germination, biological rep 1


title: Leaf tissue of Solstice at 9 weeks post germination, biological rep 1


title: Human MCF7stables cells, HAE2F1dbdmut Replicate 1

description: Human MCF7stables cells


title: Human MCF7stables cells, HAvector Replicate 1

description: Human MCF7stables cells


title: Leaf tissue of Solstice at 3 weeks post germination, biological rep 1


title: Crown tissue of Paragon at 9 weeks post germination, biological rep 1

source_name: Paragon crown 9 weeks post-germination (6 weeks vernalisation)

value: Paragon


title: Crown tissue of Paragon at 9 weeks post germination, biological rep 2


title: Leaf tissue of Solstice at 5 weeks post germination, biological rep 2

source_name: Solstice leaf 5 weeks post-germination (2 weeks vernalisation)


title: Crown tissue of Paragon at 3 weeks post germination, biological rep 2

source_name: Paragon crown 3 weeks post-germination


title: Leaf tissue of Solstice at 5 weeks post germination, biological rep 1


title: Leaf tissue of Paragon at 9 weeks post germination, biological rep 2

source_name: Paragon leaf 9 weeks post-germination (6 weeks vernaluisation)


title: Crown tissue of Paragon at 5 weeks post germination, biological rep 2

source_name: Paragon crown 5 weeks post-germination (2 weeks vernalisation)


title: Leaf tissue of Paragon at 9 weeks post germination, biological rep 1


title: Leaf tissue of Paragon at 5 weeks post germination, biological rep 1

source_name: Paragon leaf 5 weeks post-germination (2 weeks vernalisation)


title: Crown tissue of Paragon at 3 weeks post germination, biological rep 1


title: Leaf tissue of Paragon at 5 weeks post germination, biological rep 2


title: Crown tissue of Paragon at 5 weeks post germination, biological rep 1


title: Leaf tissue of Paragon at 3 weeks post germination, biological rep 1

source_name: Paragon leaf 3 weeks post-germination


title: Crown tissue of Harnesk at 5 weeks post germination, biological rep 2

source_name: Harnesk crown 5 weeks post-germination (2 weeks vernalisation)

value: Harnesk


title: Crown tissue of Harnesk at 5 weeks post germination, biological rep 1


title: Crown tissue of Harnesk at 9 weeks post germination, biological rep 1

source_name: Harnesk crown 9 weeks post-germination (6 weeks vernalisation)


title: Leaf tissue of Paragon at 3 weeks post germination, biological rep 2


title: Crown tissue of Harnesk at 9 weeks post germination, biological rep 2


title: Crown tissue of Harnesk at 3 weeks post germination, biological rep 2

source_name: Harnesk crown 3 weeks post-germination


title: Crown tissue of Harnesk at 3 weeks post germination, biological rep 1


title: Human MCF7 cells, H3K9me3 Replicate 2

description: Human MCF7 cells

source_name: MCF7 cells

tag: H3K9me3 antibody


title: Leaf tissue of Solstice at 3 weeks post germination, biological rep 2


title: Leaf tissue of Harnesk at 9 weeks post germination, biological rep 1

source_name: Harnesk leaf 9 weeks post-germination (6 weeks vernaluisation)


title: Human MCF7 cells, 5MeC Replicate 2

description: Human MCF7 cells

tag: 5MeC antibody


title: Leaf tissue of Harnesk at 3 weeks post germination, biological rep 1

source_name: Harnesk leaf 3 weeks post-germination


title: Leaf tissue of Harnesk at 5 weeks post germination, biological rep 2

source_name: Harnesk leaf 5 weeks post-germination (2 weeks vernalisation)


title: Leaf tissue of Harnesk at 5 weeks post germination, biological rep 1


title: Leaf tissue of Harnesk at 3 weeks post germination, biological rep 2


title: Human MCF7 cells, H3K27me3 Replicate 1

description: Human MCF7 cells

tag: H3K27me3 antibody


title: Testis tissue sample B

city: Chicago

first: Omar

last: De la Cruz

state: IL

address: 5734 S University Ave

department: Department of Statistics

institute: University of Chicago

description: Characterizing the expression of chimpanzee olfactory receptor genes

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RMA expression values, full model RMA background correction, quantile normalization

label: Standard Affymetrix label

organism: Pan troglodytes

source_name: Testis tissue

label_protocol: Standard Affymetrix protocol

extract_protocol: Trizol extraction

tag: From autopsy


title: Human MCF7 cells, E2F4 Replicate 1

description: Human MCF7 cells

tag: E2F4 antibody


title: Lung tissue sample B

source_name: Lung tissue


title: Lung tissue sample A


title: Human MCF7 cells, H3K27me3 Replicate 2

description: Human MCF7 cells


title: Testis tissue sample A


title: Human MCF7 cells, H3K9me3 Replicate 1

description: Human MCF7 cells


title: Heart tissue sample A

hyb_protocol: Standard Affymetrix label

scan_protocol: Standard Affymetrix label

source_name: Heart tissue

label_protocol: Standard Affymetrix label


title: Heart tissue sample B


title: Olfactory epithelium sample 2B

source_name: Olfactory epithelium


title: Liver tissue sample A

source_name: Liver tissue


title: Leaf tissue of Harnesk at 9 weeks post germination, biological rep 2


title: Liver tissue sample B


title: Human MCF7 cells, 5MeC Replicate 1

description: Human MCF7 cells


title: Olfactory epithelium sample 2A


title: Olfactory epithelium sample 1A


title: Human MCF7 cells, E2F4 Replicate 2

description: Human MCF7 cells


title: Olfactory epithelium sample 1B


title: C replicate 5

type: mixed

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

institute: University of Minnesota

description: We describe the differences in genome wide miRNA expressions between wild type 293 T mammalian cells and Ago2 transformed stable cell lines.

hyb_protocol: A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA).     Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.

scan_protocol: Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).

data_processing: BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities.  GeneSpring GX 7.3.1 (Agilent Technologies) was used for data normalization.

source_name: Total RNA from 293T transformed cells C

label_protocol: Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’.  Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.

growth_protocol: Cells are grown in DMEM with proper antibiotics

extract_protocol: Trizol® reagent (Invitrogen) was used to extract total RNA from  cells

treatment_protocol: Sample 1 control is from first replicate of 293T, 1-A, 1-B, 1-C are from the first replicate of 3 individual Ago2 transformed cells.  Sample 2 Control is from the second replicate of 293T, 2-A, 2-B, 2-C are from the second replicare of those 3  individual Ago2 transformed cells. Samples 3-, 4-, 5- are from the third, the fourth and the fifth replicates of 293T and 3 individual Ago2 transformants.

tag: miRNAs from 293T cells

label: Alexa Fluor® 647

molecule: other

organism: synthetic construct

source_name: Reference DNA

tag: synthetic DNA oligos corrresponding to human miRNAs


title: B replicate 5

source_name: Total RNA from 293T transformed cells B


title: Control replicate 5

source_name: Total RNA from 293T cells

tag: RNAs from control 293T cells


title: C replicate 4


title: A replicate 3

source_name: Total RNA from 293T transformed cells A


title: A replicate 2


title: B replicate 2


title: B replicate 4


title: C replicate 3


title: Control replicate 4


title: Control replicate 3


title: B replicate 1


title: C replicate 1


title: A replicate 1


title: A replicate 4


title: Control replicate 2


title: Control replicate 1


title: C replicate 2


title: 18-24hpa regenerating fin fold vs. control

city: Yokohama

first: Atsushi

last: Kawakami

address: 4259 Nagatsuta, Midori-ku

department: Biological Information

country: Japan

institute: Tokyo Institute of Technology

description: Gene expression profiling of zebrafish larval fin-fold regeneration comparing amputated fin fold and uncut control

hyb_protocol: According to manufacturer's instruction (performed by DNA CHIP Institute Inc. (Yokohama, Japan))

data_processing: Valid spots:　Intensity>BG+2*SD and Ch1_Intensity+Ch2_Intensity>=1000→TRUE; Values were shown only for valid spots.

organism: Danio rerio

source_name: Total RNA from regenerating 18-24hpa fin fold

label_protocol: Amino Allyl MessageAmp™ aRNA kit frim Ambion (performed by DNA CHIP Institute Inc. (Yokohama, Japan))

growth_protocol: Incubated in the egg water at 28.5 degree for 2 days before amputation

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Tissues were collected on dryice.

tag: zebrafish larval fin fold

source_name: Total RNA from control fin fold corresponding to 18-24hpa


title: control vs. 48hpa regenerating fin fold

scan_protocol: performed by DNA CHIP Institute Inc. (Yokohama, Japan)

source_name: Total RNA from control fin fold corresponding to 48hpa

source_name: Total RNA from regenerating 48hpa fin fold


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA*_delta sigB vs delta prfA delta sigB, rep3

city: Ithaca

first: Teresa

middle: M

last: Bergholz

state: NY

address: 405 Stocking Hall

department: Food Science

institute: Cornell University

description: Expression profiles were measured for 4 independent biological replicates. Array data were analyzed using a one way ANOVA model to compare differences between strains, and a two way ANOVA model to identify genes regulated by SigB and PrfA.

hyb_protocol: Microarray slide blocking was performed prior to hybridization. Slides were immersed in blocking solution (1% BSA, 5X SSC, 0.1% SDS) at 42°C. After 1 h, the slides were washed for 5 min in 0.1x SSC twice, followed by 30 sec in deionized water and then dried by centrifugation. For the strains to be compared, labeled cDNAs were combined and dried, then suspended in 50μl of hybridization buffer (5X SSC, 0.1% SDS, 0.1mM dithiothreitol (DTT), 0.5X formamide, 0.06 μg/μl salmon sperm DNA in DEPC-treated water). Samples were vortexed for 1 min and denatured at 95°C for 5 min (repeated twice), followed by a brief centrifugation, then applied to the slides using mSeries LifterSlips™ (Erie Scientific). Following overnight hybridization at 42°C, the slides were washed in 2X SSC+0.1% SDS (5 min, 42˚C), with subsequent 5-min washes at room temperature in 2X SSC+0.1% SDS, 2X SSC, and 0.2X SSC, followed by final rinse in deionized water. Slides were dried by centrifugation.

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

data_processing: Raw intensity values for all probes on each array were normalized using pin-tip LOWESS in R v.2.2.1 with the MAANOVA (v. 0.98-8) package. Signals from two replicate probes on each array were averaged and log2 transformation applied after normalization. Differences in transcript levels between strains were determined using a mixed model one way ANOVA in R/MAANOVA, where the log transformed intensity data, Y = array + dye + strain + sample (biological replicate) + E (error). Contribution of the transcriptional regulator PrfA and sigma factor SigB to changes in transcript levels was determined using a mixed model two way ANOVA, where the log transformed intensity data, Y = array + dye + prfA + sigB + prfA*sigB + sample + E. In this model, the factors prfA and sigB have two levels, determined by whether or not the protein is active or inactive. The ANOVA modeling allows for consideration of appropriate error structures for experiments with multiple sources of variation in microarray measurements. The random effects of the models were biological replicate and array effects, whereas the fixed effects were strain or prfA and sigB effects as well as dye effects. The Fs statistic, a shrinkage estimator for gene-specific variance components that makes no assumptions about the distribution of variances across genes, was estimated. Significant differences in expression between strains were determined by calculating the p-values for the Fs statistic for each gene using 1000 random permutations. The p-values were adjusted to correct for type I error with the Benjamini-Hochberg (B-H) linear step-up correction implemented in R/MAANOVA and a cutoff adjusted p-value < 0.05. Pair wise contrasts of time points were estimated by the t-test in R/MAANOVA. Contrast p-values were corrected for multiple testing by using the B-H step-up correction.

label: Alexa Fluor 532

organism: Listeria monocytogenes

source_name: Listeria monocytogenes 10403S PrfA*_delta sigB

label_protocol: cDNA was synthesized from purified total RNA and labeled with Alexa Fluor dyes using the SuperScript Plus Indirect cDNA Labeling System according to the manufacturer's protocol with following modifications. 10 μg total RNA was combined with 5μg random primers, incubated at 70°C for 10 min. Following a 5 min on ice, 6 μl 5X First-Strand buffer, 1.5 μl 0.1M dithiothreitol (DTT), 1.5 μl dNTP mix containing aminoallyl-dATP and aminohexyl-dTTP, 1 μl RNaseOUT and 2 μl SuperScript III Reverse Transcriptase were added to the reaction tube. The reverse transcription reaction was carried out at 42ºC overnight. Remaining RNA was hydrolyzed by addition of 15 μl 1N NaOH (70ºC for 10 min) and then neutralized with 15 μl 1N HCl. Each cDNA sample was purified with the QIAquick PCR purification kit (Qiagen) using RNase-free water for the final elution step. cDNA samples were dried in a SpeedVac until reduced to ~3 μl. Each cDNA sample was combined with 2X Coupling Buffer and then added to a vial of DMSO-suspended Alexa Fluor® Reactive Dye and the dye coupling reaction was carried out at room temperature for 2h. Labeled cDNA samples were purified with the QIAquick PCR purification kit with an additional 35% Guanidine-HCl wash step and a final elution step in RNase-free water. Purified, labeled cDNA was quantified with UV spectrophotometer readings at wavelengths appropriate to determine the frequency of incorporation (FOI), which is defined as the number of labeled nucleotides incorporated per 1,000 nucleotides of cDNA. cDNA samples with FOIs between 20-50 were used for microarray hybridization.

growth_protocol: Cells were grown in BHI broth at 37°C with shaking (250 rpm) unless otherwise indicated. L. monocytogenes was streaked onto brain heart infusion (BHI) agar from –80°C glycerol stock cultures followed by incubation at 37°C for 24 hr. A single colony was subsequently inoculated into BHI broth and grown overnight. An aliquot of this overnight culture was then diluted 1:100 in fresh pre-warmed BHI and grown to OD600 = 0.4, then diluted 1:100 in fresh pre-warmed BHI. After growth to early stationary phase (OD600=1.0+3hr), cells were harvested for RNA isolation.

extract_protocol: 8mL of RNAProtect was added to 4mL of stationary phase culture and vortexed. After 5 min incubation at room temperature, the bacterial cell and RNA protect mixture was centrifuged for 5 min at 5000xg and stored at -80C. RNA was isolated from frozen bacterial pellets with the Qiagen RNeasy Midi kit according to the manufacturer’s protocol for enzymatic and mechanical disruption, except that cells treated with lysozyme (20mg/ml) followed by sonication on ice for three 30 s bursts at 18–21 W (30 s pauses between bursts). Following RNA isolation, RQ1 DNase treatment (40 U; Promega) of total RNA in the presence of RNasin Plus RNA inhibitor (400 U; Promega). DNase treatment was incubated at 37°C for 1 h, followed by subsequent phenol:chloroform (2x) and 100% chloroform (1x) extractions. RNA was ethanol-precipitated overnight, centrifuged and washed with 70% ethanol, centrifuged and washed with 100% ethanol, before resuspenson of the final RNA pellet in RNase-free water. Total nucleic acid concentration and purity were estimated using absorbance readings (260/280 nm, 260/230 nm) on a NanoDrop ND-1000 spectrophotometer. RNA integrity was checked by agarose gel electrophoresis.

tag: Listeria monocytogenes 10403S PrfA* (G155S) delta sigB

tag: strain FSL B2-123

label: Alexa Fluor 635

source_name: Listeria monocytogenes 10403S delta prfA_delta sigB

tag: Listeria monocytogenes 10403S delta prfA delta sigB

tag: strain FSL B2-068


title: Human MCF7stables cells, HAvector Replicate 2

description: Human MCF7stables cells

source_name: MCF7stables cells

tag: HAvector antibody

tag: control total input


title: Human MCF7stables cells, HAE2F1dbdmut Replicate 2

description: Human MCF7stables cells

tag: HAE2F1dbdmut antibody


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA*_delta sigB vs delta prfA delta sigB, rep1


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA*_delta sigB vs delta prfA delta sigB, rep2


title: Human MCF7stables cells, HAvector Replicate 1

description: Human MCF7stables cells


title: Human MCF7stables cells, HAE2F1dbdmut Replicate 1

description: Human MCF7stables cells


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA* vs delta prfA_delta sigB, rep3

source_name: Listeria monocytogenes 10403S PrfA*

tag: Listeria monocytogenes 10403S with PrfA* (G155S) allele

tag: strain FSL B2-092


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA*_delta sigB vs delta prfA, rep3

source_name: Listeria monocytogenes 10403S delta prfA

tag: strain FSL B2-046


title: Human MCF7stables cells, HAE2F1wt Replicate 1

description: Human MCF7stables cells

tag: HAE2F1wt antibody


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA*_delta sigB vs delta prfA, rep1

tag: Listeria monocytogenes 10403S delta prfA


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA*_delta sigB vs delta prfA delta sigB, rep4


title: Listeria monocytogenes PrfA-SigB co-regulon, delta prfA vs delta prfA delta sigB, rep4


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA*_delta sigB vs delta prfA, rep4


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA* vs delta prfA_delta sigB, rep4


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA*_delta sigB vs delta prfA, rep2


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA* vs PrfA*_delta sigB, rep4


title: Listeria monocytogenes PrfA-SigB co-regulon, delta prfA vs delta prfA delta sigB, rep1


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA* vs delta prfA_delta sigB, rep1


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA* vs delta prfA_delta sigB, rep2


title: Human MCF7stables cells, HAE2F1wt Replicate 2

description: Human MCF7stables cells


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA* vs PrfA*_delta sigB, rep3


title: Listeria monocytogenes PrfA-SigB co-regulon, delta prfA vs delta prfA delta sigB, rep2


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA* vs PrfA*_delta sigB, rep2


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA* vs PrfA*_delta sigB, rep1


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA* vs delta prfA, rep3


title: 18-24hpa regenerating fin fold vs. control

source_name: Total RNA from regenerating18-24hpa fin fold


title: NIH 3T3 cells, E2F4 141180 array

description: No additional description

organism: Mus musculus

source_name: NIH 3T3

tag: E2F4 antibody

tag: Total input DNA


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA* vs delta prfA, rep2

description: Expression profiles were measured for 4 independent biological replicates.  Array data were analyzed using a one way ANOVA model to compare differences between strains, and a two way ANOVA model to identify genes regulated by SigB and PrfA.

data_processing: Raw intensity values for all probes on each array were normalized using pin-tip LOWESS in R v.2.2.1 with the MAANOVA (v. 0.98-8) package.  Signals from two replicate probes on each array were averaged and log2 transformation applied after normalization.  Differences in transcript levels between strains were determined using a mixed model one way ANOVA in R/MAANOVA, where the log transformed intensity data, Y = array + dye + strain + sample (biological replicate) + E (error).  Contribution of the transcriptional regulator PrfA and sigma factor SigB to changes in transcript levels was determined using a mixed model two way ANOVA, where the log transformed intensity data, Y = array + dye + prfA + sigB + prfA*sigB + sample + E.  In this model, the factors prfA and sigB have two levels, determined by whether or not the protein is active or inactive.  The ANOVA modeling allows for consideration of appropriate error structures for experiments with multiple sources of variation in microarray measurements.  The random effects of the models were biological replicate and array effects, whereas the fixed effects were strain or prfA and sigB effects as well as dye effects.  The Fs statistic, a shrinkage estimator for gene-specific variance components that makes no assumptions about the distribution of variances across genes, was estimated.  Significant differences in expression between strains were determined by calculating the p-values for the Fs statistic for each gene using 1000 random permutations.  The p-values were adjusted to correct for type I error with the Benjamini-Hochberg (B-H) linear step-up correction implemented in R/MAANOVA and a cutoff adjusted p-value < 0.05.  Pair wise contrasts of time points were estimated by the t-test in R/MAANOVA.  Contrast p-values were corrected for multiple testing by using the B-H step-up correction.

extract_protocol: 8mL of RNAProtect was added to 4mL of stationary phase culture and vortexed.  After 5 min incubation at room temperature, the bacterial cell and RNA protect mixture was centrifuged for 5 min at 5000xg and stored at -80C. RNA was isolated from frozen bacterial pellets with the Qiagen RNeasy Midi kit according to the manufacturer’s protocol for enzymatic and mechanical disruption, except that cells treated with lysozyme (20mg/ml) followed by sonication on ice for three 30 s bursts at 18–21 W (30 s pauses between bursts). Following RNA isolation, RQ1 DNase treatment (40 U; Promega) of total RNA in the presence of RNasin Plus RNA inhibitor (400 U; Promega). DNase treatment was incubated at 37°C for 1 h, followed by subsequent phenol:chloroform (2x) and 100% chloroform (1x) extractions. RNA was ethanol-precipitated overnight, centrifuged and washed with 70% ethanol, centrifuged and washed with 100% ethanol, before resuspenson of the final RNA pellet in RNase-free water. Total nucleic acid concentration and purity were estimated using absorbance readings (260/280 nm, 260/230 nm) on a NanoDrop ND-1000 spectrophotometer. RNA integrity was checked by agarose gel electrophoresis.


title: U133A_634A

status: Public on Sep 30 2008

city: New York

first: James

last: Korkola

address: 1275 York Ave

department: Cell Biology

institute: Memorial Sloan-Kettering

description: Adult Male Germ Cell Tumor

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA (robust multi-array) with median adjustment to match training set

source_name: U133A, 634A, pure (?) GCT (Trophoblasts, primarily cytotrophoblasts)

label_protocol: 5-12 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Frozen tissue from a germ cell tumor was minced and homogenized in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: male


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA* vs delta prfA, rep4


title: U133A_625A

description: Adult Male Germ Cell Tumor

source_name: U133A, 625A, mixed GCT (Yolk Sac, Seminoma, Teratoma)


title: U133A_630A

description: Adult Male Germ Cell Tumor

source_name: U133A, 630A, mixed GCT (Yolk Sac, Embryonal Carcinoma, Teratoma)


title: U133A_624A

description: Adult Male Germ Cell Tumor

source_name: U133A, 624A, pure GCT (Teratoma)

tag: pure GCT (Teratoma)


title: U133A_615A

description: Adult Male Germ Cell Tumor

source_name: U133A, 615A, pure GCT (Yolk Sac Tumor)

tag: pure GCT (Yolk Sac Tumor)


title: U133A_633A

description: Adult Male Germ Cell Tumor

source_name: U133A, 633A, mixed GCT (Yolk Sac, Embryonal Carcinoma, Teratoma)


title: U133A_614A

description: Adult Male Germ Cell Tumor from retroperitoneal lymph node metastasis (same patient as 208A)

source_name: U133A, 614A, pure GCT (Teratoma with secondary somatic malignancy)


title: control vs. 48hpa regenerating fin fold

tag: zebrafish larval fin fold


title: U133A_622A

description: Adult Male Germ Cell Tumor

source_name: U133A, 622A, pure GCT (Choriocarcinoma)

tag: pure GCT (Choriocarcinoma)


title: U133A_632A

description: Adult Male Germ Cell Tumor

source_name: U133A, 632A, pure GCT (Embryonal Carcinoma)

tag: pure GCT (Embryonal Carcinoma)


title: U133A_626A

description: Adult Male Germ Cell Tumor from retroperitoneal lymph node metastasis (from same patient as 231B)

source_name: U133A, 626A, mixed GCT (Yolk Sac, Embryonal Carcinoma)


title: Listeria monocytogenes PrfA-SigB co-regulon, delta prfA vs delta prfA delta sigB, rep3

tag: Listeria monocytogenes 10403S delta prfA delta sigB

tag: strain FSL B2-068


title: U133A_616A

description: Adult Male Germ Cell Tumor

source_name: U133A, 616A, pure GCT (Yolk Sac Tumor)


title: U133A_612A

description: Adult Male Germ Cell Tumor

source_name: U133A, 612A, pure GCT (Teratoma)


title: U133A_636A

description: Adult Male Germ Cell Tumor

source_name: U133A, 636A, pure GCT (Teratoma with secondary somatic malignancy)


title: U133A_617A

description: Adult Male Germ Cell Tumor

source_name: U133A, 617A, mixed GCT (Yolk Sac, Embryonal Carcinoma)


title: U133A_629A

description: Adult Male Germ Cell Tumor from retroperitoneal lymph node metastasis (from same patient as 231A)

source_name: U133A, 629A, pure GCT (Teratoma)


title: U133A_611A

description: Adult Male Germ Cell Tumor

source_name: U133A, 611A, mixed GCT (Teratoma, Yolk Sac Tumor)

tag: mixed GCT (Teratoma, Yolk Sac Tumor)


title: U133A_620A

description: Adult Male Germ Cell Tumor

source_name: U133A, 620A, mixed GCT (Embryonal Carcinoma, Seminoma)


title: U133A_638A

description: Adult Male Germ Cell Tumor

source_name: U133A, 638A, pure GCT (Teratoma with secondary somatic malignancy)


title: Listeria monocytogenes PrfA-SigB co-regulon, PrfA* vs delta prfA rep 1

source_name: Listeria monocytogenes 10403S PrfA*

source_name: Listeria monocytogenes 10403S delta prfA


title: U133A_607A

description: Adult Male Germ Cell Tumor

source_name: U133A, 607A, pure GCT (Embryonal Carcinoma)


title: U133A_610A

description: Adult Male Germ Cell Tumor

source_name: U133A, 610A, pure GCT (Teratoma with secondary somatic malignancy)


title: U133A_621A

description: Adult Male Germ Cell Tumor

source_name: U133A, 621A, pure GCT (Yolk Sac Tumor)


title: U133A_613A

description: Adult Male Germ Cell Tumor from testis (same patient as 208B)

source_name: U133A, 613A, mixed GCT (Choriocarcinoma, Embryonal Carcinoma)


title: U133A_499A

description: Adult Male Germ Cell Tumor

source_name: U133A, 499A, pure GCT (Embryonal Carcinoma)


title: Medulloblastoma sample 35

city: Rome

first: Enrico

last: De Smaele

state: Rome

address: viale Regina Elena 324

department: Experimental Medicine

country: Italy

institute: Sapienza University of Rome

data_processing: quantitative Q-PCR datas were normalized according to relative levels of RNU6 RNA (which is shown in the last row), and calibrated to the average value of the adult controls.

label: FAM

label_protocol: standard Taqman Assay

extract_protocol: total RNA was extracted by use of Trizol, according to manufacturer's protocol

tag: Medulloblastoma


title: Medulloblastoma sample 34


title: Medulloblastoma sample 36


title: Medulloblastoma sample 28


title: Medulloblastoma sample 31


title: Medulloblastoma sample 29


title: Medulloblastoma sample 30


title: U133A_608A

description: Adult Male Germ Cell Tumor

source_name: U133A, 608A, pure GCT (Teratoma with secondary somatic malignancy)


title: U133A_591A

description: Adult Male Germ Cell Tumor from mediastinum (from same patient as 186A)

source_name: U133A, 591A, mixed GCT (Yolk Sac, Embryonal Carcinoma, Teratoma)


title: Medulloblastoma sample 27


title: U133A_517B

description: Adult Male Germ Cell Tumor

source_name: U133A, 517B, pure GCT (Choriocarcinoma)


title: Medulloblastoma sample 26


title: U133A_441A

description: Adult Male Germ Cell Tumor liver metastasis (same patient as 155A)

source_name: U133A, 441A, mixed GCT (Embryonal Carcinoma, Teratoma)


title: Medulloblastoma sample 25


title: U133A_588A

description: Adult Male Germ Cell Tumor from mediastinum (from same patient as 186B)

source_name: U133A, 588A, mixed GCT (Teratoma, Choriocarcinoma, Yolk Sac, Embryonal Carcinoma)


title: Medulloblastoma sample 32


title: Medulloblastoma sample 24


title: U133A_531A

description: Adult Male Germ Cell Tumor

source_name: U133A, 531A, pure GCT (Teratoma)


title: Medulloblastoma sample 23


title: U133A_609A

description: Adult Male Germ Cell Tumor

source_name: U133A, 609A, mixed GCT (Yolk Sac, Teratoma)

tag: mixed GCT (Yolk Sac, Teratoma)


title: U133A_349C

description: Adult Male Germ Cell Tumor

source_name: U133A, 349C, GCT (Teratoma with secondary somatic malignancy)


title: U133A_606A

description: Adult Male Germ Cell Tumor

source_name: U133A, 606A, mixed GCT (Yolk Sac, Embryonal Carcinoma, Teratoma)


title: Medulloblastoma sample 21


title: U133A_490A

description: Adult Male Germ Cell Tumor

source_name: U133A, 490A, mixed GCT (Synciotrophoblasts, Yolk Sac, Embryonal Carcinoma, Teratoma)


title: Medulloblastoma sample 22


title: Medulloblastoma sample 20


title: Medulloblastoma sample 18


title: U133B_636A

description: Adult Male Germ Cell Tumor

source_name: U133B, 636A, pure GCT (Teratoma with secondary somatic malignancy)


title: U133A_393A

description: Adult Male Germ Cell Tumor from testis (same patient as 155C)

source_name: U133A, 393A, mixed GCT (Embryonal Carcinoma, Teratoma)


title: U133B_638A

description: Adult Male Germ Cell Tumor

source_name: U133B, 638A, pure GCT (Teratoma with secondary somatic malignancy)


title: Medulloblastoma sample 17


title: Medulloblastoma sample 16


title: U133B_634A

description: Adult Male Germ Cell Tumor

source_name: U133B, 634A, pure (?) GCT (Trophoblasts, primarily cytotrophoblasts)


title: Medulloblastoma sample 12


title: Medulloblastoma sample 14


title: Medulloblastoma sample 15


title: U133B_632A

description: Adult Male Germ Cell Tumor

source_name: U133B, 632A, pure GCT (Embryonal Carcinoma)


title: Medulloblastoma sample 11


title: U133B_626A

source_name: U133B, 626A, mixed GCT (Yolk Sac, Embryonal Carcinoma)


title: U133B_633A

description: Adult Male Germ Cell Tumor

source_name: U133B, 633A, mixed GCT (Yolk Sac, Embryonal Carcinoma, Teratoma)


title: Medulloblastoma sample 8


title: U133B_625A

description: Adult Male Germ Cell Tumor

source_name: U133B, 625A, mixed GCT (Yolk Sac, Seminoma, Teratoma)


title: U133B_630A

description: Adult Male Germ Cell Tumor

source_name: U133B, 630A, mixed GCT (Yolk Sac, Embryonal Carcinoma, Teratoma)


title: Medulloblastoma sample 7


title: U133B_629A

source_name: U133B, 629A, pure GCT (Teratoma)


title: Medulloblastoma sample 19


title: U133B_624A

description: Adult Male Germ Cell Tumor

source_name: U133B, 624A, pure GCT (Teratoma)


title: Medulloblastoma sample 6


title: Medulloblastoma sample 9


title: Medulloblastoma sample 5


title: U133B_621A

description: Adult Male Germ Cell Tumor

source_name: U133B, 621A, pure GCT (Yolk Sac Tumor)


title: Medulloblastoma sample 3


title: Medulloblastoma sample 4


title: U133B_620A

description: Adult Male Germ Cell Tumor

source_name: U133B, 620A, mixed GCT (Embryonal Carcinoma, Seminoma)


title: Contol fetal cerebellum 5

source_name: ctrl fetal 5

tag: Contol fetal cerebellum


title: U133B_615A

description: Adult Male Germ Cell Tumor

source_name: U133B, 615A, pure GCT (Yolk Sac Tumor)


title: U133B_614A

source_name: U133B, 614A, pure GCT (Teratoma with secondary somatic malignancy)


title: U133B_613A

source_name: U133B, 613A, mixed GCT (Choriocarcinoma, Embryonal Carcinoma)


title: Medulloblastoma sample 1


title: U133B_612A

description: Adult Male Germ Cell Tumor

source_name: U133B, 612A, pure GCT (Teratoma)


title: Contol fetal cerebellum 4

source_name: ctrl fetal 4


title: U133B_622A

description: Adult Male Germ Cell Tumor

source_name: U133B, 622A, pure GCT (Choriocarcinoma)


title: Contol fetal cerebellum 1

source_name: ctrl fetal1


title: Contol fetal cerebellum 3

source_name: ctrl fetal3


title: Contol fetal cerebellum 2

source_name: ctrl fetal2


title: U133B_611A

description: Adult Male Germ Cell Tumor

source_name: U133B, 611A, mixed GCT (Teratoma, Yolk Sac Tumor)


title: U133B_617A

description: Adult Male Germ Cell Tumor

source_name: U133B, 617A, mixed GCT (Yolk Sac, Embryonal Carcinoma)


title: U133B_609A

description: Adult Male Germ Cell Tumor

source_name: U133B, 609A, mixed GCT (Yolk Sac, Teratoma)


title: Contol adult cerebellum 9

source_name: ctrl adult9

tag: Contol adult cerebellum


title: Contol adult cerebellum 8

source_name: ctrl adult8


title: U133B_616A

description: Adult Male Germ Cell Tumor

source_name: U133B, 616A, pure GCT (Yolk Sac Tumor)


title: U133B_606A

description: Adult Male Germ Cell Tumor

source_name: U133B, 606A, mixed GCT (Yolk Sac, Embryonal Carcinoma, Teratoma)


title: Medulloblastoma sample 2


title: U133B_591A

source_name: U133B, 591A, mixed GCT (Yolk Sac, Embryonal Carcinoma, Teratoma)


title: Contol adult cerebellum 5

source_name: ctrl adult5


title: U133B_588A

source_name: U133B, 588A, mixed GCT (Teratoma, Choriocarcinoma, Yolk Sac, Embryonal Carcinoma)


title: U133B_607A

description: Adult Male Germ Cell Tumor

source_name: U133B, 607A, pure GCT (Embryonal Carcinoma)


title: U133B_610A

description: Adult Male Germ Cell Tumor

source_name: U133B, 610A, pure GCT (Teratoma with secondary somatic malignancy)


title: Contol adult cerebellum 7

source_name: ctrl adult7


title: U133B_608A

description: Adult Male Germ Cell Tumor

source_name: U133B, 608A, pure GCT (Teratoma with secondary somatic malignancy)


title: Medulloblastoma sample 10


title: Contol adult cerebellum 6

source_name: ctrl adult6


title: U133B_517B

description: Adult Male Germ Cell Tumor

source_name: U133B, 517B, pure GCT (Choriocarcinoma)


title: Contol adult cerebellum 1

source_name: ctrl adult1


title: Contol adult cerebellum 4

source_name: ctrl adult4


title: Contol adult cerebellum 2

source_name: ctrl adult2


title: U133B_393A

source_name: U133B, 393A, mixed GCT (Embryonal Carcinoma, Teratoma)


title: U133B_441A

source_name: U133B, 441A, mixed GCT (Embryonal Carcinoma, Teratoma)


title: U133B_499A

description: Adult Male Germ Cell Tumor

source_name: U133B, 499A, pure GCT (Embryonal Carcinoma)


title: Contol adult cerebellum 3

source_name: ctrl adult3


title: NIH 3T3 cells, E2F4 141269 array

description: No additional description

source_name: NIH 3T3

tag: Total  input DNA


title: U133B_349C

description: Adult Male Germ Cell Tumor

source_name: U133B, 349C, GCT (Teratoma with secondary somatic malignancy)


title: U133B_490A

description: Adult Male Germ Cell Tumor

source_name: U133B, 490A, mixed GCT (Synciotrophoblasts, Yolk Sac, Embryonal Carcinoma, Teratoma)


title: TumPancM17 (single-channel-Median-Norm-Intensity)

status: Public on Sep 15 2008

city: Phoenix

first: Yoga

last: Balagurunathan

state: AZ

address: 445 N. Fifth street

institute: TGEN

description: Pancreatic Tumor samples with mix of human normals arrayed on Agilent oligo (v1:18K probes&v2:22k probes)platform, single channel extracted median standardized, control removes,common arrays combined to reduced number (~17l)

hyb_protocol: Agilent In-situ hybridization

scan_protocol: Agilent scanner.

data_processing: The data were obtained with the Agilent Feature Extration Algorithm/Software v5.x,v6.x,v7.x,v8.x,v9.x. The raw data was standardized by each chip median value to cross compare arrays. Common probes taken from tow versions (Agilent human v1&v2) chips, repeating Q/Cl probes replaced by median values other control probes removed.

label: Cy3 or Cy5

source_name: primary pancreatic tumor

label_protocol: Agilent lowRNA input labeling

extract_protocol: Trizol


title: TumPancM19 (single-channel-Median-Norm-Intensity)


title: TumPancM14 (single-channel-Median-Norm-Intensity)


title: TumPancM15 (single-channel-Median-Norm-Intensity)


title: TumPancM20 (single-channel-Median-Norm-Intensity)


title: TumPancM18 (single-channel-Median-Norm-Intensity)


title: TumPancM10 (single-channel-Median-Norm-Intensity)


title: TumPancM16 (single-channel-Median-Norm-Intensity)


title: TumPancM12 (single-channel-Median-Norm-Intensity)


title: TumPancM13 (single-channel-Median-Norm-Intensity)


title: TumPancM8 (single-channel-Median-Norm-Intensity)


title: U133B_531A

description: Adult Male Germ Cell Tumor

source_name: U133B, 531A, pure GCT (Teratoma)


title: TumPancM9 (single-channel-Median-Norm-Intensity)


title: TumPancM7 (single-channel-Median-Norm-Intensity)


title: TumPANT5 (single-channel-Median-Norm-Intensity)


title: TumPancM6 (single-channel-Median-Norm-Intensity)


title: TumPancM4 (single-channel-Median-Norm-Intensity)


title: TumPancM5 (single-channel-Median-Norm-Intensity)


title: TumPancM11 (single-channel-Median-Norm-Intensity)


title: TumPANT8 (single-channel-Median-Norm-Intensity)


title: TumPancM3 (single-channel-Median-Norm-Intensity)


title: TumPancM2 (single-channel-Median-Norm-Intensity)


title: TumPancM1 (single-channel-Median-Norm-Intensity)


title: TumPANT4 (single-channel-Median-Norm-Intensity)


title: TumPANT6 (single-channel-Median-Norm-Intensity)


title: TumPANT7 (single-channel-Median-Norm-Intensity)


title: TumPANT3 (single-channel-Median-Norm-Intensity)


title: TumPANT2 (single-channel-Median-Norm-Intensity)


title: NormSkin2 (single-channel-Median-Norm-Intensity)

source_name: normal tissue


title: NormSkmuscle1 (single-channel-Median-Norm-Intensity)


title: NormSaliv3 (single-channel-Median-Norm-Intensity)


title: NormOvary10 (single-channel-Median-Norm-Intensity)


title: NormSkin1 (single-channel-Median-Norm-Intensity)


title: NormThyroid1 (single-channel-Median-Norm-Intensity)


title: NormUterus1 (single-channel-Median-Norm-Intensity)


title: NormOvary8 (single-channel-Median-Norm-Intensity)


title: NormOvary11 (single-channel-Median-Norm-Intensity)


title: NormOvary13 (single-channel-Median-Norm-Intensity)


title: NormOvary4 (single-channel-Median-Norm-Intensity)


title: TumPANT1 (single-channel-Median-Norm-Intensity)


title: NormOvary5 (single-channel-Median-Norm-Intensity)


title: NormOvary6 (single-channel-Median-Norm-Intensity)


title: NormOvary3 (single-channel-Median-Norm-Intensity)


title: NormKidney8 (single-channel-Median-Norm-Intensity)


title: NormKidney9 (single-channel-Median-Norm-Intensity)


title: NormOvary2 (single-channel-Median-Norm-Intensity)


title: NormLung2 (single-channel-Median-Norm-Intensity)


title: NormOvary9 (single-channel-Median-Norm-Intensity)


title: NormKidney6 (single-channel-Median-Norm-Intensity)


title: NormOvary12 (single-channel-Median-Norm-Intensity)


title: NormLung3 (single-channel-Median-Norm-Intensity)


title: NormKidney7 (single-channel-Median-Norm-Intensity)


title: NormGallbladder3 (single-channel-Median-Norm-Intensity)


title: NormCervical1 (single-channel-Median-Norm-Intensity)


title: NormBreast6 (single-channel-Median-Norm-Intensity)


title: NormCartilage2 (single-channel-Median-Norm-Intensity)


title: NormGallbladder2 (single-channel-Median-Norm-Intensity)


title: NormGallbladder1 (single-channel-Median-Norm-Intensity)


title: NormColon5 (single-channel-Median-Norm-Intensity)


title: NormColon4 (single-channel-Median-Norm-Intensity)


title: NormBreast4 (single-channel-Median-Norm-Intensity)


title: NormEsophagus1 (single-channel-Median-Norm-Intensity)


title: NormBreast5 (single-channel-Median-Norm-Intensity)


title: NormBrain14 (single-channel-Median-Norm-Intensity)


title: NormBrain13 (single-channel-Median-Norm-Intensity)


title: NormIleum1 (single-channel-Median-Norm-Intensity)


title: NormColon3 (single-channel-Median-Norm-Intensity)


title: NormBrain15 (single-channel-Median-Norm-Intensity)


title: NormBrain16 (single-channel-Median-Norm-Intensity)


title: NormBladder2 (single-channel-Median-Norm-Intensity)


title: NormBreast3 (single-channel-Median-Norm-Intensity)


title: NormBladder1 (single-channel-Median-Norm-Intensity)


title: NormAdrenal6 (single-channel-Median-Norm-Intensity)


title: NormBreast2 (single-channel-Median-Norm-Intensity)


title: NormBladder3 (single-channel-Median-Norm-Intensity)


title: NormOvary7 (single-channel-Median-Norm-Intensity)


title: NormAdrenal3 (single-channel-Median-Norm-Intensity)


title: NormAdrenal4 (single-channel-Median-Norm-Intensity)


title: NormAdipose3 (single-channel-Median-Norm-Intensity)


title: NormAstrocytoma1 (single-channel-Median-Norm-Intensity)


title: NormAdrenal5 (single-channel-Median-Norm-Intensity)


title: NormStomach1 (single-channel-Median-Norm-Intensity)


title: NormPANN2 (single-channel-Median-Norm-Intensity)


title: NormPANN3 (single-channel-Median-Norm-Intensity)


title: NormAdipose1 (single-channel-Median-Norm-Intensity)


title: NormTcell1 (single-channel-Median-Norm-Intensity)


title: NormPANN1 (single-channel-Median-Norm-Intensity)


title: NormTcell2 (single-channel-Median-Norm-Intensity)


title: NormSkeletal (single-channel-Median-Norm-Intensity)


title: NormTcell34 (single-channel-Median-Norm-Intensity)


title: NormOsteoblast (single-channel-Median-Norm-Intensity)


title: NormLung (single-channel-Median-Norm-Intensity)


title: NormBrain (single-channel-Median-Norm-Intensity)


title: NormCartilage (single-channel-Median-Norm-Intensity)


title: NormAdipose2 (single-channel-Median-Norm-Intensity)


title: NormAdrenal12 (single-channel-Median-Norm-Intensity)


title: NormMonocyte12 (single-channel-Median-Norm-Intensity)


title: NormSalivary2 (single-channel-Median-Norm-Intensity)


title: NormColon2 (single-channel-Median-Norm-Intensity)


title: NormTesticular (single-channel-Median-Norm-Intensity)


title: NormVein (single-channel-Median-Norm-Intensity)


title: NormPANN4 (single-channel-Median-Norm-Intensity)


title: NormGastic (single-channel-Median-Norm-Intensity)


title: NormOvary (single-channel-Median-Norm-Intensity)


title: NormSalivary1 (single-channel-Median-Norm-Intensity)


title: NormColon1 (single-channel-Median-Norm-Intensity)


title: Whitefish  backcross individual 494

status: Public on Sep 01 2008

city: Quebec

first: Andrew

middle: R

last: Whiteley

state: Quebec

address: Pavillon Marchand

department: Biologie

country: Canada

institute: Universite Laval

description: One of backcross individuals used in analysis.  Data from each channel were averaged to obtain normalized score shown in data matrix

hyb_protocol: Hybridization followed the procedures at http://web.uvic.ca/cbr/grasp/ (Genisphere Array 50 Protocol).

scan_protocol: Scanned with a ScanArray Express scanner (Packard Bioscience). Spot location and quantification (mean intensity for each spot) was performed with QuantArray© (Perkin Elmer).

data_processing: Aberrant spot signals were removed before analysis and their values were estimated using the “K-Nearest Neighbors Imputer” function implemented in SAM software (Tusher et al 2001). Genes with intensity less than the mean of the empty spot controls plus 2.5 times their standard deviation were removed from the analysis. According to this criterion, 3,563 among the 16,006 transcripts passed this threshold and were considered for subsequent analyses. After correcting for local background, raw intensity values were both log2 transformed and normalized using the regional LOWESS method implemented in the R/MANOVA software (Kerr et al. 2000), available at: http://www.jax.org/staff/churchill/labsite/software/Rmaanova.

organism: Coregonus clupeaformis

source_name: Total RNA from whole whitefish brains

label_protocol: Reverse transcriptase PCR was performed using 15 μg of total RNA per sample following the SuperScript II Reverse Transcriptase protocol (Invitrogen life technologies). Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).

extract_protocol: Dissected brain tissue (250-350 mg) was sampled for 55 individuals from the hybrid x dwarf backcross mapping family, and stored at - 80°C until RNA extraction. RNA was extracted according to the Trizol Reagent protocol (Gibco BRL) and quantified with a GeneQuant spectrometer (Pharmacia), and RNA integrity was verified with a 2100 Bioanalyzer (Agilent).

treatment_protocol: Brains were dissected from whole frozen fish kept at -80deg.C.

tag: Whitefish  backcross individual 494


title: Whitefish  backcross individual 496

tag: Whitefish  backcross individual 496


title: NormMelanocyte (single-channel-Median-Norm-Intensity)


title: Whitefish  backcross individual 492

tag: Whitefish  backcross individual 492


title: Whitefish  backcross individual 499

tag: Whitefish  backcross individual 499


title: M1 MGAS5005 vs. trxR mutant #2ds

city: College Park

first: Kevin

middle: S

last: McIver

state: MD

address: 3124 Biociences Research Bldg. (413)

department: Cell Biology and Molecular Genetics

institute: University of Maryland, College Park

description: Details located in Ribardo et al, 2006

hyb_protocol: Equal volumes (25 ul) of labeled Cy5 cDNA and Cy3 cDNA were dried under vacuum, resuspended in 23.8 ul of dH2O and boiled for 5 min followed by cooling on ice for 1 min. 5x Hyb Buffer (GE Healthcare- 17 ul) and formamide (27.2 ul) was added to the cDNA and applied to array slides under raised cover slip (Lifterslip, Inc). Microarray slides were hybridized at 50°C overnight in slide chambers (Array It). Slides were washed twice for 10 min each in the following buffer concentrations and temperatures: 6X SSPE/0.01% Tween-20 at 50°C, 0.8X SSPE/0.001% Tween-20 at 50°C, and 0.8X SSPE at RT.

scan_protocol: genepix 6.1

data_processing: ratio-based Pearson Centered normalization using Acuity 4.0

organism: Streptococcus pyogenes

source_name: M1 MGAS5005.trxR

label_protocol: Ambion Amino Allyl cDNA labeling Kit

growth_protocol: 37c in closed cap tubes to late exponential phase

extract_protocol: Triton-X100 RNA isolation

tag: M1 MGAS5005.trxR (trxR-) Biological replicate 2

source_name: M1 MGAS5005

tag: M1 MGAS5005 Biological replicate 2


title: M1 MGAS5005 vs. trxR mutant #3

description: Details located in Ribardo et al, 2006

tag: M1 MGAS5005 Biological replicate 3

tag: M1 MGAS5005.trxR (trxR-) Biological replicate 3


title: M1 MGAS5005 vs. trxR mutant #2

description: Details located in Ribardo et al, 2006

tag: M1 MGAS5005 Biological Replicate 2

tag: M1 MGAS5005.trxR (trxR-) Biological Replicate 2


title: M1 MGAS5005 vs. trxR mutant #3ds

description: Details located in Ribardo et al, 2006


title: M1 MGAS5005 vs. trxR mutant #1

description: Details in Ribardo et al, 2006

label_protocol: Ambion Amino Allyl cDNA labeling kit

growth_protocol: 37C in closed cap tubes to late exponential phase

tag: M1 MGAS5005 Biological replicate #1

tag: M1 MGAS5005.trxR (trxR-) Biological replicate #1


title: M1 MGAS5005 vs. trxR mutant 1ds

description: Details in Ribardo et al, 2006

tag: M1 MGAS5005.trxR (trxR-) Biological replicate 1

tag: M1 MGAS5005 Biological replicate 1


title: Whitefish  backcross individual 484

tag: Whitefish  backcross individual 484


title: Whitefish  backcross individual 480

tag: Whitefish  backcross individual 480


title: Whitefish  backcross individual 489

tag: Whitefish  backcross individual 489


title: Whitefish  backcross individual 443

tag: Whitefish  backcross individual 443


title: Whitefish  backcross individual 487

tag: Whitefish  backcross individual 487


title: Whitefish  backcross individual 478

tag: Whitefish  backcross individual 478


title: Whitefish  backcross individual 473

tag: Whitefish  backcross individual 473


title: Whitefish  backcross individual 482

tag: Whitefish  backcross individual 482


title: Whitefish  backcross individual 460

tag: Whitefish  backcross individual 460


title: Whitefish  backcross individual 445

tag: Whitefish  backcross individual 445


title: Whitefish  backcross individual 472

tag: Whitefish  backcross individual 472


title: Whitefish  backcross individual 439

tag: Whitefish  backcross individual 439


title: Whitefish  backcross individual 438

tag: Whitefish  backcross individual 438


title: Whitefish  backcross individual 428

tag: Whitefish  backcross individual 428


title: Whitefish  backcross individual 429

tag: Whitefish  backcross individual 429


title: Whitefish  backcross individual 424

tag: Whitefish  backcross individual 424


title: Whitefish  backcross individual 422

tag: Whitefish  backcross individual 422


title: Whitefish  backcross individual 419

tag: Whitefish  backcross individual 419


title: Whitefish  backcross individual 397

tag: Whitefish  backcross individual 397


title: Whitefish  backcross individual 417

tag: Whitefish  backcross individual 417


title: Whitefish  backcross individual 411

tag: Whitefish  backcross individual 411


title: Whitefish  backcross individual 408

tag: Whitefish  backcross individual 408


title: Whitefish  backcross individual 394

tag: Whitefish  backcross individual 394


title: Whitefish  backcross individual 392

tag: Whitefish  backcross individual 392


title: Whitefish  backcross individual 393

tag: Whitefish  backcross individual 393


title: Whitefish  backcross individual 415

tag: Whitefish  backcross individual 415


title: Whitefish  backcross individual 352

tag: Whitefish  backcross individual 352


title: Whitefish  backcross individual 391

tag: Whitefish  backcross individual 391


title: Whitefish  backcross individual 350

tag: Whitefish  backcross individual 350


title: Whitefish  backcross individual 367

tag: Whitefish  backcross individual 367


title: Whitefish  backcross individual 379

tag: Whitefish  backcross individual 379


title: Whitefish  backcross individual 377

tag: Whitefish  backcross individual 377


title: Whitefish  backcross individual 396

tag: Whitefish  backcross individual 396


title: Whitefish  backcross individual 343

tag: Whitefish  backcross individual 343


title: Whitefish  backcross individual 384

tag: Whitefish  backcross individual 384


title: Whitefish  backcross individual 385

tag: Whitefish  backcross individual 385


title: Whitefish  backcross individual 389

tag: Whitefish  backcross individual 389


title: Whitefish  backcross individual 341

tag: Whitefish  backcross individual 341


title: Whitefish  backcross individual 418

tag: Whitefish  backcross individual 418


title: Whitefish  backcross individual 333

tag: Whitefish  backcross individual 333


title: Whitefish  backcross individual 319

tag: Whitefish  backcross individual 319


title: Whitefish  backcross individual 314

tag: Whitefish  backcross individual 314


title: Whitefish  backcross individual 313

tag: Whitefish  backcross individual 313


title: Whitefish  backcross individual 435

tag: Whitefish  backcross individual 435


title: Whitefish  backcross individual 286

tag: Whitefish  backcross individual 286


title: Whitefish  backcross individual 293

tag: Whitefish  backcross individual 293


title: Whitefish  backcross individual 273

tag: Whitefish  backcross individual 273


title: Whitefish  backcross individual 266

tag: Whitefish  backcross individual 266


title: Whitefish  backcross individual 257

tag: Whitefish  backcross individual 257


title: Whitefish  backcross individual 251

tag: Whitefish  backcross individual 251


title: Whitefish  backcross individual 253

tag: Whitefish  backcross individual 253


title: 155/33-F677: condition: L-HE 03

city: saint-pée sur nivelle

first: catherine

last: kolditz

address: quartier Ibarron

country: France

institute: INRA

description: Microarray hybridization were performed at the INRA UMR1067 transcriptome facility (St-Pée-sur-Nivelle. France). The hybridization procedure was performed as described in Panserat et al., 2008.

hyb_protocol: Six hepatic RNA samples from each experimental condition were used for microarray hybridization at the INRA UMR1067 transcriptome facility (St-Pée-sur-Nivelle. France). A first hybridisation was performed at 42°C for 48h using 33P-labelled T7 promoter oligonucleotide (5~-CACTATAGGGAATTTGGCC-3~) to estimate the amount of cDNA in each spot. After stripping (3 hours 68°C. 0.1X SSC. 0.2% SDS), hybridisations with hepatic cDNAs have been performed. Microarrays were prehybridised  for 1h at 65°C in hybridisation buffer (5X Denhardt. 5X SSC. 0.5% SDS). RNA was degraded by treatment at 68°C for 30 min with 1 ml 10% SDS. 1 ml 0.5M EDTA and 3 ml 3M NaOH.a nd then equilibrated at room temperature for 15 min. Neutralization was done by adding 10ml 1M Tris-HCl plus 3 ml 2N HCl. Microarrays were then incubated with the corresponding denatured labelled cDNA for 18 h at 65°C in hybridisation solution. After 3 washes (1h 68°C with 0.X SSC 0.2% SDS), microarrays were exposed 65 hours to phosphor-imaging plates that were scanned using a FUJI BASS 5000.

scan_protocol: Scanner: BAS-5000 Fuji - Feature extraction software: AGScan

data_processing: Liver sample number 677 (L-HE group) have been hybridized with the membrane number 33 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

organism: Oncorhynchus mykiss

source_name: L-HE group, third tank liver sample number 677  description: lean muscle line (L line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.

label_protocol: Labelled cDNAs were prepared from 5 µg of RNA by simultaneous reverse transcription and labelling for 1 hour at 42°C in the presence of 50µCi [alpha-33P] dCTP, 5 µM dCTP and 800 µM each dATP. dGTP and dTTP and 200 units SuperScriptTM III Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA)  in 30 µL final volume.

extract_protocol: Total RNAs were extracted from liver using the TRIzol reagent method (Invitrogen, Carlsbad, CA). Nine individual samples per experimental condition were used as biological replicates. Total RNA was quantified using spectrophotometry based on absorbance at 260 nm, and integrity was controlled using the Agilent 2100 bioanalyzer (Agilent Technologies, Kista, Sweden).

tag: condition

value: L-HE 03


title: 155/18-F637: condition: L-HE 02

data_processing: Liver sample number 637 (L-HE group) have been hybridized with the membrane number 18 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-HE group, second tank liver sample number 637  description: lean muscle line (L line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.

value: L-HE 02


title: 155/68-F582: condition: L-LE 01

data_processing: Liver sample number 582 (L-LE group) have been hybridized with the membrane number 68 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-LE group, first tank liver sample number 582  description: lean muscle line (L line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.

value: L-LE 01


title: 155/17-F639: condition: L-HE 02

data_processing: Liver sample number 639 (L-HE group) have been hybridized with the membrane number 17 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: liver sample number 639  description: lean muscle line (L line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.


title: 155/12-F545: condition: F-HE 01

data_processing: Liver sample number 545 (F-HE group) have been hybridized with the membrane number 12 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-HE group, first tank liver sample number 545  description: Fatty muscle line (F line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.

value: F-HE 01


title: 155/07-F603: condition: F-HE 02

data_processing: Liver sample number 603 (F-HE group) have been hybridized with the membrane number 07 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-HE group, second tank liver sample number 603  description: Fatty muscle line (F line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.

value: F-HE 02


title: 155/72-F714: condition: F-LE 01

data_processing: Liver sample number 714 (F-LE group) have been hybridized with the membrane number 72 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-LE group, first tank liver sample number 714  description: fatty muscle line (F line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.

value: F-LE 01


title: 155/45-F509: condition: L-LE 03

data_processing: Liver sample number 509 (L-LE group) have been hybridized with the membrane number 45 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-LE group, third tank liver sample number 509  description: lean muscle line (L line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.

value: L-LE 03


title: 155/08-F542: condition: F-HE 01

data_processing: Liver sample number 542 (F-HE group) have been hybridized with the membrane number 08 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-HE group, first tank liver sample number 542  description: Fatty muscle line (F line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.


title: 155/14-F697: condition: F-HE 03

data_processing: Liver sample number 697 (F-HE group) have been hybridized with the membrane number 14 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-HE group, third tank liver sample number 697  description: Fatty muscle line (F line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.

value: F-HE 03


title: 155/11-F717: condition: F-LE 01

data_processing: Liver sample number 717 (F-LE group) have been hybridized with the membrane number 11 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-LE group, first tank liver sample number 717  description: fatty muscle line (F line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.


title: 155/53-F620: condition: L-LE 02

data_processing: Liver sample number 620 (L-LE group) have been hybridized with the membrane number 53 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-LE group, liver sample number 620  description: lean muscle line (L line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.

value: L-LE 02


title: 155/40-F660: condition: F-LE 03

data_processing: Liver sample number 660 (F-LE group) have been hybridized with the membrane number 40 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-LE group, third tank liver sample number 660  description: fatty muscle line (F line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.

value: F-LE 03


title: 155/39-F694: condition: F-HE 03

data_processing: Liver sample number 694 (F-HE group) have been hybridized with the membrane number 39 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-HE group, third tank liver sample number 694  description: Fatty muscle line (F line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.


title: 155/19-F580: condition: L-LE 01

data_processing: Liver sample number 580 (L-LE group) have been hybridized with the membrane number 19 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-LE group, first tank liver sample number 580  description: lean muscle line (L line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.


title: 155/23-F562: condition: L-HE 01

data_processing: Liver sample number 562 (L-HE group) have been hybridized with the membrane number 23 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-HE group, first tank liver sample number 562  description: lean muscle line (L line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.

value: L-HE 01


title: 155/20-F584: condition: L-LE 01

data_processing: Liver sample number 584 (L-LE group) have been hybridized with the membrane number 20 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-LE group, first tank liver sample number 584  description: lean muscle line (L line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.


title: 155/24-F525: condition: F-LE 02

data_processing: Liver sample number 525 (F-LE group) have been hybridized with the membrane number 24 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-LE group, second tank liver sample number 525  description: fatty muscle line (F line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.

value: F-LE 02


title: 155/28-F563: condition: L-HE 01

data_processing: Liver sample number 563 (L-HE group) have been hybridized with the membrane number 28 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-HE group, first tank liver sample number 563  description: lean muscle line (L line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.


title: 155/05-F527: condition: F-LE 02

data_processing: Liver sample number 527 (F-LE group) have been hybridized with the membrane number 05 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-LE group, second tank liver sample number 527  description: fatty muscle line (F line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.


title: 155/13-F676: condition: L-HE 03

data_processing: Liver sample number 676 (L-HE group) have been hybridized with the membrane number 13 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-HE group, third tank liver sample number 676  description: lean muscle line (L line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.


title: 155/34-F678: condition: L-HE 03

data_processing: Liver sample number 678 (L-HE group) have been hybridized with the membrane number 34 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-HE group, third tank liver sample number 678  description: lean muscle line (L line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.


title: 155/55-F640: condition: L-HE 02

data_processing: Liver sample number 640 (L-HE group) have been hybridized with the membrane number 55 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-HE group, second tank liver sample number 640  description: lean muscle line (L line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.


title: 155/54-F657: condition: F-LE 03

data_processing: Liver sample number 657 (F-LE group) have been hybridized with the membrane number 54 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-LE group, third tank liver sample number 657  description: fatty muscle line (F line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.


title: 155/65-F601: condition: F-HE 02

data_processing: Liver sample number 601 (F-HE group) have been hybridized with the membrane number 65 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-HE group, second tank liver sample number 601  description: Fatty muscle line (F line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.


title: 155/56-F618: condition: L-LE 02

data_processing: Liver sample number 618 (L-LE group) have been hybridized with the membrane number 56 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-LE group, second tank liver sample number 618  description: lean muscle line (L line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.


title: 155/66-F504: condition: L-LE 03

data_processing: Liver sample number 504 (L-LE group) have been hybridized with the membrane number 66 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-LE group, third tank liver sample number 504  description: lean muscle line (L line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.


title: 155/60-F505: condition: L-LE 03

data_processing: Liver sample number 505 (L-LE group) have been hybridized with the membrane number 60 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: L-LE group, third tank liver sample number 505  description: lean muscle line (L line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.


title: 155/62-F523: condition: F-LE 02

data_processing: Liver sample number 523 (F-LE group) have been hybridized with the membrane number 62 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-LE group, second tank liver sample number 523  description: fatty muscle line (F line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.


title: 155/61-F715: condition: F-LE 01

data_processing: Liver sample number 715 (F-LE group) have been hybridized with the membrane number 61 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-LE group, first tank liver sample number 715  description: fatty muscle line (F line), fed a low fat diet (LE diet, containing 10% lipids) from the first feeding for 6 months.


title: 155/59-F698: condition: F-HE 03

data_processing: Liver sample number 698 (F-HE group) have been hybridized with the membrane number 59 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-HE group, third tank liver sample number 698  description: Fatty muscle line (F line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.


title: 155/67-F546: condition: F-HE 01

data_processing: Liver sample number 546 (F-HE group) have been hybridized with the membrane number 67 from the CRB's membrane serie n°155 - Spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array.

source_name: F-HE group, first tank liver sample number 546  description: Fatty muscle line (F line), fed a high fat diet (HE diet, containing 23% lipids) from the first feeding for 6 months.