title: Chlamydophila pneumoniae infection 120+/-DAM hpi vs. 48 hpi (02-29-A2)

status: Public on May 15 2007

city: Berlin

first: André

middle: Paul

last: Mäurer

address: Charitéplatz 1

department: Molecular Biology

institute: Max Planck Institute for Infection Biology

hyb_protocol: Arrays were blocked prior to hybridization by incubation for 45 min at 42°C in blocking solution (4x SSC, 0.5% SDS, 1% BSA), washed five times with H20 and dried by centrifugation (1000 rpm, RT, 2 min). Microarray experiments were done as two-color hybridizations. In order to compensate for dye-specific effects and to ensure statistically relevant data, a color swap was performed. Reverse transcribed cDNA pools were mixed with hybridization buffer (Ambion), denatured, snap-cooled, pipetted onto the array using Lifter Slips (Erie, USA) and placed in a sealed humidified hybridization chamber (Scienion, Germany) at 42° C for 48 hours without shaking. After hybridization the array was washed and dried according to the Ambion protocol.

scan_protocol: Scanning of microarrays was performed with 5 μm resolution using a microarray laser scanner (Agilent).

data_processing:
Features were extracted using the Agilent Technologies image analysis
software (Version A7.5) using default settings for non-Agilent microarrays. A local background subtraction method was used and the background was adjusted globally to zero. Dye normalization was done using the rank consistency method and applying a local weighted regression normalization (LOWESS). The ratio between both channels, the log ratio error and the p-values were calculated using default settings. Data analysis was carried
out on the Rosetta Inpharmatics platform Resolver Buildt 4.2.

organism: Chlamydia pneumoniae

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 120+/-DAM hpi (persistent infection recovered after 72 hpi).

label_protocol:
A modified protocol for indirect incorporation of aminoallyl nucleotides during a first-strand reverse transcription reaction was established to yield a maximum of labeled cDNA copies of the total RNA pool for Cpn. Each labeling reaction consisted of 20 μg of total RNA (1 μg/μl)
(or the yield of 50 μg total RNA processed with the Microbeenrich procedure), 2 μg random nonamer primers (Amersham, USA), 4.0 ml of dNTP master mix, and 2 μl (4 units/μl) of Superscript II reverse transcriptase (Stratagene). RNA and primers were heated to 65° C for 10 min slowly cooled to room temperature, snap cooled on ice before the remaining
components were added and incubated at 42° C for 2h. RNA was degraded by adding 10 μl (2.5 M) NaOH, incubating at 37° C for 15 min and neutralizing with 20 μl (2 M) HEPES. cDNA was precipitated by adding 6 μl (3 M) sodiumacetate and 150 μl EtOH, then incubated
at -20° C overnight and pelleted with 13,000 rpm at 4° C. The pellet was resuspended in 0.1 M sodiumbicarbonate buffer (pH 9.0), added to either Cy 3 or Cy 5 mono NHS esters (Amersham), incubated at room temperature for 90 min and purified using 30K Microcon spin columns (Millipore, USA). The elution volume was diluted using hybridization buffer
(Ambion) and quantified at A552nm for Cy 3 and A650nm for Cy 5.

growth_protocol: The CWL029 Cpn strain (ATCC VR1310) was propagated in HEp-2 cells. Cells were infected with a multiplicity of infection (MOI) of 2 in RPMI medium without supplements, centrifuged at 37°C for 1 h at 2,100 revolutions per min (rpm), and incubated at 35° C and 5 % CO2 for 1 h. Afterwards, medium was replaced with RPMI medium supplemented with 5 % fbs, containing  cycloheximide (chex) (1 μg/ml). Cultures were incubated for 72 h at 35° C, harvested using glass beads (Sigma, Germany) and the supernatant transferred to a 50 ml tube (Greiner, Germany). Host cells were lysed using glass beads (Sigma, Germany) and centrifuged at 800 rpm for 10 min to pellet cell debris. The supernatant was centrifuged at 10,000 rpm for 1h to pellet EB. The pellet was washed with sucrose phosphate glutamate buffer (SPG, pH 7.4), recentrifuged and resolved in SPG-buffer, aliquoted and stored at –80° C. Stocks were determined to be free of mycoplasma contamination. For acute and persistent infections HEp-2 cells were infected with Cpn at a MOI of 40 for the 6 and 12 hpi time points, and an MOI of 15 for all other time points. The time course started upon infection (Fig. 1). To generate persistent infections 30 μM of deferoxamine (DAM) was added to the medium throughout the infection process starting at the time of infection. Cells were incubated at 35°C and 5% CO2 until the respective time points, washed with prewarmed PBS and harvested with 1 ml TRIzol (Invitrogen, Germany) per well. The bacteria were examined by staining cell cultures grown on coverslips with an anti-LPS antibody (Progen, Germany) to confirm proper growth and establishment of acute and persistent infections.

extract_protocol: Cpn-infected HEp-2 cells were lysed with TRIzol. Total RNA was isolated using a modified protocol. For a detailed description of the modified protocol see the supplementary data. Integrity of the total RNA was verified using the Bioanalyzer 2100 (Agilent, USA), and RNA was quantified by photometer and Nanodrop (Kisker,Germany) measurements prior to labeling. In addition, 50 μg total RNA for the 6 and 12 hpi time points was hybridized with 20 μg of total RNA from the 48 hpi time point, and was purified using the Microbeenrich (Ambion, USA) procedure to increase signal intensities.

treatment_protocol: For acute and persistent infections HEp-2 cells were infected with Cpn at a MOI of 40 for the 6 and 12 hpi time points, and an MOI of 15 for all other time points. The time course started upon infection. To generate persistent infections 30 μM of deferoxamine (DAM) was added to the medium throughout the infection process starting at the time of infection. Cells were incubated at 35° C and 5% CO2 until the respective time points, washed with prewarmed PBS and harvested with 1 ml TRIzol (Invitrogen, Germany) per well. The bacteria were examined by staining cell cultures grown on coverslips with an anti-LPS antibody (Progen, Germany) to confirm proper growth and establishment of acute and persistent infections.

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 120 hpi of the recovered persistent infection.

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 48 hpi (acute infection).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 48 hpi of the acute infection.


title: Chlamydophila pneumoniae infection 48 hpi vs. 120+/-DAM hpi (02-41-A1)

type: RNA

state: Berlin

country: Germany

molecule: total RNA


title: Profiling RB for miRNAs_RB sample 2386

status: Public on May 20 2007

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

description: Samples GSM169532&GSM169534, GSM169533&GSM170986, and GSM169535&GSM170842 represent sample RNAs cohybridized on the same two-color array.  However, the data were treated as single channel data not as ratio data.

hyb_protocol: miRNA-labeling, reverse transcription, mRNA isolation, cDNA labeling, and hybridization were carried out as described previously (Babak et al., 2004; Zhang et al., 2004). Following labeling, samples were resuspended in 0.5 mL of hybridization buffer (1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate, pH 6.5, 33% formamide and 40ug salmon sperm DNA), and hybridized on a rotating platform for 16-24 h at 42°C. Slides were washed (rocking ~30 seconds in 6x SSPE, 0.005% sarcosine, ~30 seconds in 0.06x SSPE).

scan_protocol: Slides were scanned with an Axon 4000A microarray scanner (Axon Instruments, Union City, CA).

data_processing: arcsinh (normalized,spatially detrended absolute intensity)

label: Alexa Fluor 546 or 647

organism: Homo sapiens

label_protocol: miRNA-labeling, reverse transcription, mRNA isolation, cDNA labeling, and hybridization were carried out as described previously (Babak et al., 2004; Zhang et al., 2004). In brief, for miRNA profiling, 7ug of DNAse treated (Fermentas) total RNA was chemically labeled with Ulysis Alexa Fluor 546/647 kits (Invitrogen) according to manufacturer’s instructions. For mRNA profiling, cDNA was generated and labeled as described (Zhang et al., 2004).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.


title: Chlamydophila pneumoniae infection 48 hpi vs. 96+/-DAM hpi (03-28-A1)

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 96+/-DAM hpi (persistent infection recovered after 72 hpi).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 96 hpi of the recovered persistent infection.


title: In vitro angiogenesis at 1hr, biological rep 3

city: Aurora

first: Allan

middle: Ray

last: Albig

state: CO

department: Pharmacology

country: USA

institute: University of Colorado Health Sciences

description:
no additional information
Angiogenesis on Matrigel 1hr

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

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: MAS 5

label: biotin

organism: Mus musculus

source_name: Murine MB114 microvascular Endothelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: MB114 cells were split 1:3 24 hours prior to culture on Matrigel matrix

extract_protocol: Ambion RNAqueus kit, phenol chloroform extraction, Quiagen Rneasy kit

treatment_protocol: Matrigel cultures were harvested after 1, 5, 15, 25 hours on Matrigel

tag: Angiogenesis on Matrigel 1hr


title: Chlamydophila pneumoniae infection 72 hpi vs. 72+DAM hpi (05-62-A1)

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 72 hpi (acute infection).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 72 hpi of the acute infection.

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 72+DAM hpi (persistent infection).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 72 hpi of the persistent infection.


title: Chlamydophila pneumoniae infection 48+DAM hpi vs. 48 hpi (03-57-A2)

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 48+DAM hpi (persistent infection).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 48 hpi of the persistent infection.


title: Chlamydophila pneumoniae infection 96+/-DAM hpi vs. 48 hpi (03-29-A2)


title: Chlamydophila pneumoniae infection 72 hpi vs. 72+DAM hpi (03-21-A1)


title: Chlamydophila pneumoniae infection 48+DAM hpi vs. 48 hpi (03-30-A2)


title: Chlamydophila pneumoniae infection 72+DAM hpi vs. 72 hpi (05-63-A2)


title: Chlamydophila pneumoniae infection 72 hpi vs. 72+DAM hpi (03-11-A1)


title: Profiling RB for miRNAs_normal retina_repeat1

source_name: Normal retina (1/3)

tag: This is one of three miRNA profiling repeats of human normal retina.


title: Chlamydophila pneumoniae infection 72+DAM hpi vs. 72 hpi (03-22-A2)


title: Chlamydophila pneumoniae infection 48+DAM hpi vs. 48 hpi (03-13-A2)


title: Chlamydophila pneumoniae infection 72+DAM hpi vs. 72 hpi (03-12-A2)


title: Chlamydophila pneumoniae infection 48 hpi vs. 48+DAM hpi (03-14-A1)


title: Chlamydophila pneumoniae infection 24+DAM hpi vs. 24 hpi (03-18-A2)

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 24+DAM hpi (acute infection).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 24 hpi of the persistent infection.

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 24 hpi (acute infection).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 24 hpi of the acute infection.


title: Chlamydophila pneumoniae infection 48 hpi vs. 48+DAM hpi (03-23-A1)


title: Chlamydophila pneumoniae infection 24 hpi vs. 24+DAM hpi (03-64-A1)

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 24+DAM hpi (persistent infection).


title: Chlamydophila pneumoniae infection 24 hpi vs. 24+DAM hpi (05-15-A1)


title: Chlamydophila pneumoniae infection 72 hpi vs. 48 hpi (03-61-A2)


title: Chlamydophila pneumoniae infection 24+DAM hpi vs. 24 hpi (03-65-A2)


title: Chlamydophila pneumoniae infection 48 hpi vs. 48+DAM hpi (03-19-A1)


title: Chlamydophila pneumoniae infection 24 hpi vs. 24+DAM hpi (03-17-A1)

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 24 hpi of the peristent infection.


title: Chlamydophila pneumoniae infection 48 hpi vs. 72 hpi (03-35-A1)


title: Chlamydophila pneumoniae infection 24+DAM hpi vs. 24 hpi (03-16-A2)


title: Chlamydophila pneumoniae infection 72 hpi vs. 48 hpi (03-36-A2)


title: Chlamydophila pneumoniae infection 36 hpi vs. 48 hpi (03-42-A2)

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 36 hpi (acute infection).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 36 hpi of the acute infection.


title: Chlamydophila pneumoniae infection 48 hpi vs. 60 hpi (03-26-A1)

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 60 hpi (acute infection).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 60 hpi of the acute infection.


title: Chlamydophila pneumoniae infection 48 hpi vs. 60 hpi (03-37-A1)


title: Chlamydophila pneumoniae infection 48 hpi vs. 72 hpi (03-26-A1)


title: Chlamydophila pneumoniae infection 60 hpi vs. 48 hpi (03-51-A2)


title: Chlamydophila pneumoniae infection 60 hpi vs. 48 hpi (03-44-A2)


title: Chlamydophila pneumoniae infection 60 hpi vs. 48 hpi (04-20-A2)


title: Chlamydophila pneumoniae infection 48 hpi vs. 36 hpi (03-27-A1)


title: Chlamydophila pneumoniae infection 36 hpi vs. 48 hpi (03-28-A2)


title: Chlamydophila pneumoniae infection 48 hpi vs. 36 hpi (03-12-A1)


title: Chlamydophila pneumoniae infection 48 hpi vs. 72 hpi (03-60-A1)


title: Chlamydophila pneumoniae infection 72 hpi vs. 48 hpi (03-27-A2)


title: Chlamydophila pneumoniae infection 24 hpi vs. 48 hpi (04-10-A2)


title: Chlamydophila pneumoniae infection 24 hpi vs. 48 hpi (03-55-A2)


title: Chlamydophila pneumoniae infection 48 hpi vs. 24 hpi (04-09-A1)


title: Chlamydophila pneumoniae infection 24 hpi vs. 48 hpi (04-25-A2)


title: Chlamydophila pneumoniae infection 24 hpi vs. 48 hpi (03-58-A2)


title: Chlamydophila pneumoniae infection 18 hpi vs. 48 hpi (03-16-A2)

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 18 hpi (acute infection).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 18 hpi of the acute infection.


title: Chlamydophila pneumoniae infection 48 hpi vs. 24 hpi (03-33-A1)


title: Chlamydophila pneumoniae infection 48 hpi vs. 18 hpi (03-15-A1)


title: Chlamydophila pneumoniae infection 48 hpi vs. 24 hpi (03-59-A1)


title: Chlamydophila pneumoniae infection 48 hpi vs. 24 hpi (03-24-A1)


title: Chlamydophila pneumoniae infection 48 hpi vs. 12 hpi (04-26-A1)

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 12 hpi (acute infection).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 12 hpi of the acute infection.


title: Chlamydophila pneumoniae infection 18 hpi vs. 48 hpi (03-32-A2)


title: Chlamydophila pneumoniae infection 6 hpi vs. 48 hpi (04-28-A2)

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 6 hpi (acute infection).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 6 hpi of the acute infection.


title: Chlamydophila pneumoniae infection 12 hpi vs. 48 hpi (04-27-A2)


title: Chlamydophila pneumoniae infection 12 hpi vs. 48 hpi (04-22-A2)


title: Chlamydophila pneumoniae infection 48 hpi vs. 12 hpi (03-45-A1)


title: Chlamydophila pneumoniae infection 48 hpi vs. 6 hpi (04-23-A1)


title: Chlamydophila pneumoniae infection 48 hpi vs. 60 hpi (03-43-A1)


title: Chlamydophila pneumoniae infection 18 hpi vs. 48 hpi (03-53-A2)


title: Chlamydophila pneumoniae infection 48 hpi vs. 12 hpi (04-21-A1)


title: Chlamydophila pneumoniae infection 48 hpi vs. 6 hpi (04-15-A1)


title: Chlamydophila pneumoniae infection 6 hpi vs. 48 hpi (04-24-A2)


title: Chlamydophila pneumoniae infection 48 hpi vs. 18 hpi (03-54-A1)


title: Chlamydophila pneumoniae infection 48 hpi vs. 36 hpi (03-41-A1)


title: Chlamydophila pneumoniae infection 12 hpi vs. 48 hpi (03-25-A2)


title: Chlamydophila pneumoniae infection 48 hpi vs. 12 hpi (03-24-A1)


title: Chlamydophila pneumoniae infection 48 hpi vs. 6 hpi (04-29-A1)

growth_protocol:
The CWL029 Cpn strain (ATCC VR1310) was propagated in HEp-2 cells. Cells were infected with a multiplicity of infection (MOI) of 2 in RPMI medium without supplements, centrifuged at 37°C for 1 h at 2,100 revolutions per min (rpm), and incubated at 35° C and 5 % CO2 for 1 h.
Afterwards, medium was replaced with RPMI medium supplemented with 5 % fbs, containing  cycloheximide (chex) (1 μg/ml). Cultures were incubated for 72 h at 35° C, harvested using glass beads (Sigma, Germany) and the supernatant transferred to a 50 ml tube (Greiner,
Germany). Host cells were lysed using glass beads (Sigma, Germany) and centrifuged at 800 rpm for 10 min to pellet cell debris. The supernatant was centrifuged at 10,000 rpm for 1h to pellet EB. The pellet was washed with sucrose phosphate glutamate buffer (SPG, pH 7.4), recentrifuged and resolved in SPG-buffer, aliquoted and stored at –80° C. Stocks were
determined to be free of mycoplasma contamination. For acute and persistent infections HEp-2 cells were infected with Cpn at a MOI of 40 for the 6 and 12 hpi time points, and an MOI of 15 for all other time points. The time course started upon infection (Fig. 1). To generate persistent infections 30 μM of deferoxamine (DAM) was added to the medium
throughout the infection process starting at the time of infection. Cells were incubated at 35° C and 5% CO2 until the respective time points, washed with prewarmed PBS and harvested with 1 ml TRIzol (Invitrogen, Germany) per well. The bacteria were examined by staining cell cultures grown on coverslips with an anti-LPS antibody (Progen, Germany) to confirm proper growth and establishment of acute and persistent infections.

treatment_protocol:
For acute and persistent infections HEp-2 cells were infected with Cpn at a MOI of 40 for the 6 and 12 hpi time points, and an MOI of 15 for all other time points. The time course started upon infection. To generate persistent infections 30 μM of deferoxamine (DAM) was added to the medium
throughout the infection process starting at the time of infection. Cells were incubated at 35° C and 5% CO2 until the respective time points, washed with prewarmed PBS and harvested with 1 ml TRIzol (Invitrogen, Germany) per well. The bacteria were examined by staining cell cultures grown on coverslips with an anti-LPS antibody (Progen, Germany) to confirm proper growth and establishment of acute and persistent infections.


title: Chlamydophila pneumoniae infection 48 hpi vs. 18 hpi (03-31-A1)


title: Chlamydophila pneumoniae infection 12 hpi vs. 48 hpi (03-19-A2)


title: HSC_2Months_B

status: Public on Jun 01 2007

city: Houston

first: Stuart

last: Chambers

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: LT-Hematopoietic stem cell isolated by flow cytometry

hyb_protocol: Standard protocol from manufacturer (Affymetrix)

scan_protocol: Hardware: GeneChip¨ Scanner 3000

data_processing: Normalization was done with the GCRMA package from Bioconductor

label: Biotin

molecule: polyA RNA

source_name: Hematopoietic stem cells

label_protocol: Second round of MessageAmp(Ambion) amplification was biotinylated with bio-CTP and bio-UTP per manufature's protocol.

extract_protocol: 25,000- 50,000 cells were FACS sorted, RNA was isolated with RNAqueous Kit (Ambion) per manufacture's protocol, DNAse treated with DNAse1, phenol:chloroform:isoamyl alcohol extracted, and amplified through two rounds of in vitro transcription using MessageAmp (Ambion) per manufacture's protocol

tag: Strain

value: C57Bl/6, Gender:male, Age:2-months-old


title: expression profiling of pob3 vs wt E020F#27

status: Public on May 10 2007

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description: expression profiling of pob3 vs wt

hyb_protocol: Xue Y. et al Yeast (2004)

scan_protocol: chip reader

data_processing: Genespring

organism: Schizosaccharomyces pombe

source_name: wt sample

label_protocol: Xue Y. et al Yeast (2004)

extract_protocol: Xue Y. et al Yeast (2004)

tag: wt sample

tag: pob3 sample


title: Expression profiling of pob3 vs wt E020F#28

description: expression profiling of pob3 vs wt

scan_protocol: Imagene 4.2

source_name: wt


title: Chlamydophila pneumoniae infection 6 hpi vs. 48 hpi (04-17-A2)

source_name: HEp-2 cells infected with Chlamydophila pneumoniae at 48 hpi (acute infection).

tag: Hep-2 (ATCC-CCL23) cells infected with C.pneumoniae CWL029 (0hpi). Samples were lysed at 48 hpi of the acute infection.


title: CHC358T-U133A

status: Public on May 01 2007

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

description: Detailed procedure is provided in the supplemental experimental procedures in [Rebouissou et al., J Biol Chem 2007, PMID: 17379603].

hyb_protocol: Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).

scan_protocol: Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).

data_processing: Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the R package affy [Gautier et al., Bioinformatics 2004, 20: 307-15], available as part of the Bioconductor project [Gentleman et al., Genome Biol 2004, 5: R80], and the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm using a background adjusted PM intensities model [Irizarry et al., Nucleic Acids Research 2003, 31: e15], and with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].

label_protocol: For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).

extract_protocol: Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.

tag: Sample

tag: Gender

value: female;

tag: Age at onset

value: 46 years;

tag: Disease

value: hepatocellular adenoma;

tag: Tissue

value: tumor liver;

tag: HNF1-alpha status

value: gene mutation.


title: CHC373T-U133A

value: 44 years;


title: TGF-beta treated skin keratinocyte cells at 12hr_Exp1

city: Bangalore

first: Paturu

last: Kondaiah

address: C.N.R. Rao Circle

department: Molecular Reproduction, Development and Genetics

country: India

institute: Indian Institute of Science

description: no additional information is necessary

hyb_protocol: The hybridisation was carried out in the GeneTAC Hyb Station (Genomic solutions, UK) at 650 for 4 hours, 600 for 4 hours and 550 for 10 hours. The slides were then washed with medium stringency (2X SSC and 0.1% SDS), high stringency (0.1X SSC and 0.1% SDS) and post wash (0.1X SSC) buffers for 5 minutes each, dried and scanned using a Scanner (Scanarray Express, Perkin Elmer life Sciences, USA).

scan_protocol: Scanned using Scanarray Express (Perkin Elmer Life Sci), the software used for image aquisition was scanarray.

data_processing: All the image analyses have been done using the Quantarray software (Perkin Elmer Life Sciences, USA). Filtering and compilation of data have been done using Microsoft Excel and Microsoft Access. Spots of compromised quality and with low intensity  were eliminated from the analysis. The data was normalized by LOWESS method (Avadis 3.1, Strand Life Sciences, India), Cy5:Cy3 ratios were established and log2 values were calculated.

source_name: skin keratinocyte cells control

label_protocol: The labelling of the probe was done using the Micromax direct labelling kit (Perkin Elmer Life Sci.) according to the recommended protocol.

growth_protocol: Cells were plated in tissue culture dishes in DMEM with 10% heat inactivated Fetal Bovine Serum and other constituents, incubated at 37 degrees C in 5% CO2 and 90% humidity.

extract_protocol: RNA was Extracted using TRI reagent from Sigma Aldrich with an extra chloroform extraction and cleaned up using RNA easy mini columns.RNA was quantitated on a spectrophotometer and analyzed on a formaldehyde-agarose gel.

treatment_protocol: No treatment (Control for 5ng/ml TGF-beta1treatment), grown in recommended medium, washed with serum free medium and allowed to remain in serum free medium for 12hr before extraction of the sample.

tag: immortalized skin keratinocyte cells

source_name: skin keratinocyte cells TGF-beta treated

treatment_protocol: Cells grown in recommended medium, washed with serum free medium and treated with 5ng/ml TGF-beta1 in serum free medium, for 12hr before extraction of the sample.

tag: immortalized skin keratinocytes


title: CHC465T-U133A

value: 52 years;


title: TGF-beta treated skin keratinocyte cells at 1hr Exp2

description: no additional information is necessary

treatment_protocol: No treatment (Control for 5ng/ml TGF-beta1treatment), grown in recommended medium, washed with serum free medium and allowed to remain in serum free medium for 1hr before extraction of the sample.

treatment_protocol: Cells grown in recommended medium, washed with serum free medium and treated with 5ng/ml TGF-beta1 in serum free medium, for 1hr before extraction of the sample.

tag: Immortalized skin keratinocyte cells


title: TGF-beta treated skin keratinocyte cells at 12hr_Exp2

description: no additional information is necessary


title: CHC373T-Cy5

description:
For more details on microarray procedures, see Graudens et al. Genome Biol (2006) 7:R19.
Quality Controls of RNA samples: Concentration and purity of the RNA preparation was checked first by UV-spectrophotometry using the Ultrospec3100 pro (GE Healthcare, USA) and 5-mm cuvettes. The absorbance (A) was measured from 200 nm to 350 nm. A235, A260, A280 and A320 were determined and A260:A280 ratios were calculated. Quality of each total RNA was measured by microfuidic/capillary electrophoresis using RNA 6000 Nano LabChip® kits with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA), and the results assessed by human inspection and with two-user independent classifiers evaluation as described previously [Imbeaud et al., NAR, 2005]. Only samples that reached the anticipated purity and integrity parameters (RIN >= 6; DegFact <= 13) were introduced within the microarray pipeline process. Quality Controls of IVT transcription: Double stranded cDNA (ds-cDNA) and amplified RNA (aRNA) products were analyzed for purity and concentration by UV spectrophotometry, using the Ultrospec3100 pro and 5-mm cuvettes (GE Healthcare, USA). The absorbance (A) was measured from 200 nm to 350 nm. A235, A260, A280 and A320 were determined and A260:A280 ratios were calculated. Three metrics were considered based on the A260 measurement. First, efficiency of the reverse transcription (ds-cDNA quantity/total RNA quantity) and IVT (aRNA quantity/ds-cDNA quantity) reaction efficiencies were computed. The yield of amplification was quantified (aRNA quantity/mRNA quantity), with the assumption that total RNA contains 2% of mRNA. Finally, an aliquot (1 µl) of the IVT reaction was loaded onto RNA 6000 Nano Labchip® using a Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The chip was prepared according to the manufacturer’s protocol. An mRNA nano assay was run on the chip, and the size of the aRNA was compared with the molecular weight markers. On one hand, ds-cDNA product with unsatisfactory reverse transcription reaction efficiency (RT ≤ 0.4) and purity (A260:A280 ratios ≤ 1.6) were removed from the IVT reaction pipeline. On the other hand, aRNA products with unsatisfactory yield of amplification (amplification < 1,000) and integrity (mean size < 1,000 nucleotides) were removed from subsequent analyses. Only samples that reached the expected purity and integrity parameters described above were introduced within the microarray labeling and hybridization pipelines. Quality Controls of Cy-Dye target labeling: Purity and concentration of each target was checked by UV spectrophotometry, using the Ultrospec3100 pro and 70-mm cuvettes (GE Healthcare). Based on the absorbance measured at 256 nm, 550 nm and 650 nm and considering extinction factor for Cy3- and Cy5-dye respectively of 0.15 and 0.25, the yield of cDNA synthesis and dye incorporation rate were computed. An aliquot (1 µl) of the purified labeling reaction was loaded onto RNA 6000 Nano Labchip® using a Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The chip was prepared according to the manufacturer’s protocol and a mRNA nano assay was run on the chip. The shape and sizes of the Cy-dye targets were compared with the molecular weight markers. Targets with unsatisfactory yield of incorporation (dye incorporation rate < 10; A256:A550 or 650 < 2) and integrity (size < 200 nucleotides) were removed from subsequent analyses. The shape of the Cy-dye probes should present a smeared profile with no clearly identified additional peaks.

hyb_protocol: A mixture of equimolar aliquots (20 pmol) of each labeled target (DATA and REF) was incubated at 95°C for 4 min in the presence of 1.5 µg Oligo-A80 (Eurogentec, USA) and 1 µg human Cot-I DNA® (Invitrogen, USA). Fragmented labeled cDNA was then placed onto 11K_VJF-ARRAY slides in a 30 µl hybridization solution (50% formamide, GE Healthcare, USA) and covered by a coverslip. The slides were subsequently hybridized in a humid hybridization cabinet (GE Healthcare, USA) for 16 hr at 42°C. Then the hybridized slides were washed in 1xSSC, 0.2% SDS for 10 min at 55°C, twice in 0.1x SSC, 0.2% SDS for 10 min at 55°C and twice in 0.1x SSC for 1 min at room temperature.

scan_protocol: After washing and drying, the arrays were scanned at 532 nm (PMT 600 V) and 635 nm (PMT 650 V) using a 3rd generation array scanner (GE Healthcare, USA) and independent grayscale images (8 bits, Tiff) were generated for each pair of samples to be compared.

data_processing: Foreground (raw) data - ARMDens - were local background-subtracted (corners between spots - median value) and normalized using a Lowess (locally weighted linear regression) transformation. The following selection criteria were applied: all spots having a mean signal (after background subtraction) less than that of the background and below that of the negative controls in both Cy3 and Cy5 channels were systematically excluded; the data were also filtered to exclude spots flagged as missing or corrupted in one array. We next calculated the expression ratios (DATA/REF) in all analyses; the provided VALUE corresponds to the log, base 2 ratios. Replicate spots on the array (n=2) are considered separately.

label_protocol: Linear Amplification: One-round of RNA amplification was performed on total RNA as described in [Van Gelder et al., 1990; Eberwine et al., 1992] with some modifications. Amplified RNA products were air dried, resuspended in 10µl RNase-free water and then stored at -80°C; 1 µl of the reaction (1/10) was stored to perform quality assessment (Purity, size, yield). Labeling protocol: Targets were synthesized using 1.0 µg amplified RNA, 1 µl anchored oligo-(dT) and 2 µl random nonamers (GE Healthcare, USA) for priming (total volume 11 µl, 10 min, 70°C) in presence of 1 µl spike RNA from Lucidea™ Microarray Human Scorecard v1.1 (GE Healthcare, USA). cDNA products were generated using 1 mM of either Cy3- or Cy5-dCTP (GE Healthcare, USA) and 200 units MMLV RNase H- reverse transcriptase (Promega, USA) at 42°C for 2 to 3 hr. After reverse transcription, the RNA was degraded by adding 2 µl of 2.5 N NaOH and incubating at 37°C for 10 min. The reaction was then neutralized by adding 10 µl of 2 M MOPS (free acid) and Cy3- and Cy5-containing targets were purified twice onto QIAquick PCR columns (Qiagen, Germany) according the manufacturer’s instructions with minor modifications. The Cy-dye targets were controlled during quality assessment (purity, size, yield). Adjusted Cy-dye target yield was calculated to reflect carryover of unlabeled aRNA. Thus, certified targets were air-dried in a vacuum centrifuge for 1.5 hr and resuspended in RNase-free water to reach a 10 pmol/µl concentration.

extract_protocol: see Provider description

tag: Universal Reference RNA


title: CHC476T-Cy5

value: 30 years;


title: CHC474T-Cy5

value: 45 years;


title: TGF-beta treated skin keratinocyte cells at 1hr_Exp1

description: no additional information is necessary

source_name: keratinocyte cells control

source_name: keratinocyte cells TGF-beta treated


title: CHC357T-Cy5

value: 28 years;


title: CHC358T-Cy5


title: CHC369T-Cy5

value: 40 years;


title: CHC474T-U133A


title: CHC474N-Cy5

value: non tumoral liver.


title: CHC463T-Cy5

value: 34 years;


title: CHC340T-U133A

value: male;

value: 23 years;


title: CHC373N-Cy5


title: CHC476N-Cy5


title: TGF-beta treated skin keratinocyte cells at 4hr_Exp2

description: no additional information is necessary

treatment_protocol: No treatment (Control for 5ng/ml TGF-beta1treatment), grown in recommended medium, washed with serum free medium and allowed to remain in serum free medium for 4hr before extraction of the sample.

treatment_protocol: Cells grown in recommended medium, washed with serum free medium and treated with 5ng/ml TGF-beta1 in serum free medium, for 4hr before extraction of the sample.


title: TGF-beta treated skin keratinocyte cells at 4hr_Exp1

description: no additional information is necessary

source_name: skin keratinocyte cells TGF beta treated


title: CHC464N-Cy5


title: CHC462N-Cy5


title: CHC369N-Cy5


title: CHC465T-Cy5


title: CHC369T-Cy3


title: CHC465T-Cy3


title: CHC476T-Cy3


title: CHC358T-Cy3


title: CHC357N-Cy5


title: CHC358N-Cy5


title: CHC476N-Cy3


title: CHC464N-Cy3


title: CHC373N-Cy3


title: CHC462N-Cy3


title: CHC474T-Cy3


title: CHC474N-Cy3


title: CHC463T-Cy3


title: CHC357T-Cy3


title: CHC358N-Cy3


title: CHC373T-Cy3


title: ko_epid-dox

city: Bonn

first: Hong

last: Lu

state: NRW

address: Nussallee 11

institute: University of Bonn

description: Microarray and TaqMan real-time PCR showed  MMp-13 and IL-beta were significantly downregulated after doxycycline treatment in  EBS mouse model – keratin5 knockout mice.

hyb_protocol: Following fragmentation, 8 microg of cRNA were hybridized to the Affymetrix  MGU74Av2 microarrays  according to the protocols provided by the manufacturer

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

data_processing: The data were condensed with MAS 5.0 by BioChip-Labor, University Essen Medical Centre. The normalization target was set to 1000.

source_name: mouse epidermis from keratin5 knockout(K5-/-) mice not treated

label_protocol: Biotinylated cRNA were prepared from 2 microg total RNA using the BioArray-High-Yield-RNA-Transcript-Labeling-Kit (Enzo, Farmingdale, NY).

extract_protocol: K5-/- epidermis was removed from neonatal mice and immediately frozen in liquid nitrogen. RNA was extracted with TRIzol reagent (Life Technologies-BRL, Karlsruhe, Germany) according to the protocol of the supplier. Six animals were included in the group. All the total RNA samples were  pooled.

tag: 5 % sucrose solution was administered by oral route to pregnant K5+/- females (mated to K5+/- males) starting from E13.5.  This was the control group.


title: ko_skin

description: By investigating differentiated expressed genes after loss of Keratin 5, we found out that TNF pathway genes were not involved in EBS mouse model and local inflammation factor IL-1beta,IL-6 were upregulated.

source_name: mouse epidermis from keratin5 knockout(K5-/-) mouse

extract_protocol: Skin from K5-/- mice  was removed from neonatal mice and immediately frozen in liquid nitrogen.RNA was extracted with TRIzol reagent (Life Technologies-BRL, Karlsruhe, Germany) according to the protocol of the supplier.  Six animals were included in the group. All the total RNA samples  were pooled for later microarray experiments.  As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

tag: keratin knockout mouse


title: wt_skin

source_name: mouse epidermis from wildtype mouse

extract_protocol: Skin from wildtype mice  was removed from neonatal mice and immediately frozen in liquid nitrogen.RNA was extracted with TRIzol reagent (Life Technologies-BRL, Karlsruhe, Germany) according to the protocol of the supplier.  Six animals were included in the group. All the total RNA samples  were pooled for later microarray experiments.  As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

tag: wild type mouse


title: CHC369N-Cy3


title: CHC357N-Cy3


title: ko_epid+dox

source_name: mouse epidermis from keratin5 knockout(K5-/-) mice after doxycycline treatment

extract_protocol: K5-/- epidermis treated with doxycycline were removed  from neonatal mice and immediately frozen in liquid nitrogen. Six animals were included in the group. All the total RNA samples were isolated with TRIzol reagent (Life Technologies-BRL, Karlsruhe, Germany) according to the protocol of the supplier. Then they were pooled.

tag: doxycycline (50 µg/mlwith 5 % sucrose) was administered by oral route to pregnant K5+/- females (mated to K5+/- males) starting from E13.5.


title: I-205 versus C100 Rev ( HV3-20-38 )

status: Public on Apr 30 2007

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

description: I-205 versus C100 Rev

hyb_protocol: The combined Cy3 and Cy5 labeled cDNAs are put in a total volume of 250 ul DEPC H20 and 250 ul of 2X Agilent hybridization buffer. The mixture is then denatured for 2 minutes and applied on the Agillent hybridization chamber/gasket slide in sandwich with the array slide. The hybridization is performed at 65 degre for 16 hours.

scan_protocol: Agilent Scanner

data_processing: IPLab/DeArray image microarray analysis software

source_name: Human Breast cancer cell line

label_protocol: 15 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Aminoallyl dUTP, after NaOH RNA hydrolysis, the labeled Aminoallyl dUTP cDNA is purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104). The Aminoallyl dUTP cDNAs are then coupled with either Cy3 or Cy5 mono NHS Ester Dyes. The CyDyes labeled cDNAs are then purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104).

extract_protocol: RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns

tag: Human Breast cancer cell line


title: S-22 versus C100 Rev ( HV3-20-46 )

description: S-22 versus C100 Rev


title: I-205 versus C100 ( HV3-20-37 )

description: I-205 versus C100


title: S-22 versus C100 ( HV3-20-35 )

description: S-22 versus C100


title: S-22 versus C100 Rev ( HV3-20-36 )

description: S-22 versus C100 Rev


title: I-205 versus C100 ( HV3-20-47 )

description: I-205 versus C100


title: I-205 versus C100 Rev ( HV3-20-49 )

description: I-205 versus C100 Rev


title: H1-177 versus C100 ( HV3-20-33 )

description: H1-177 versus C100


title: H1-177 versus C100 Rev ( HV3-20-34 )

description: H1-177 versus C100 Rev


title: R48A

city: Odense

first: Mads

last: Thomassen

address: Soender Boulevard 9

department: Clinical Genetics (KKA)

country: Denmark

institute: Odense University Hospital

description: Biochem Biophys Res Comm 2006; 344: 1111-1120

data_processing: VSN normalised

source_name: breast tumor

tag: breast tumor

source_name: ref. RNA

tag: Ref RNA


title: R48B


title: R15B


title: R15A


title: H1-177 versus C100 Rev ( HV3-20-44 )

description: H1-177 versus C100 Rev


title: R42B


title: R41A


title: R14B


title: R13B


title: R13A


title: R12B


title: R12A


title: R14A


title: S-22 versus C100 ( HV3-20-45 )

description: S-22 versus C100


title: R11B


title: R11A


title: R10B


title: R10A


title: R8A


title: R9A


title: R9B


title: R5B


title: R1A

description: Biochem Biophys Res Comm 2006; 344:1111-1120


title: R5A


title: R2A


title: R2B


title: R4B


title: R6B


title: R4A


title: R42A


title: R6A


title: R8B


title: R7A


title: R1B

tag: Breast tumor


title: L31B

description: Biochem Biophys res comm 2006; 344:1111-1120


title: L31A


title: L33A


title: R7B


title: L33B


title: L30A


title: L30B


title: L29A


title: L26B


title: L29B


title: L16B


title: L27A


title: R41B


title: L26A


title: L27B


title: L9A


title: H3med

city: Chicago

first: Zarema

middle: H

last: Arbieva

state: IL

address: 835 S. Wolcott A301

department: RRC

institute: UIC

hyb_protocol: Affymetrix Midi Euk2v3 hybridization

scan_protocol: Affymetrix CEL analysis

data_processing: RMA, quantile normalization

source_name: cultured PBMC, nontreated

label_protocol: Affymetrix IVT labeling

growth_protocol: BBMC cells were suspended at 1 x 106 cells/ml in complete RPMI supplemented with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, and 100 µg/mL streptomycin. 107 cells were placed in two 10 cm tissue culture plates. Cells were incubated at 37°C in humidified air containing 8% CO2 for 18 hours.

extract_protocol: Total cellular RNA was isolated by using Trizol® Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

treatment_protocol: 15µM,2,4-benzenetriol was added to the cell suspension in one plate. Untreated cells in the second plate served as a control for basal levels of gene expression.

tag: cultured PBMC, nontreated


title: L14A


title: L2A

tag: ref RNA


title: H5med


title: L1A


title: L11A


title: H4med


title: L16A


title: L9B


title: H5bt5

source_name: cultured PBMC, treated with Bt5

tag: cultured PBMC, treated with Bt5


title: L7B


title: C4med


title: L2B


title: C5med


title: C7med


title: L11B


title: H2bt5


title: L14B


title: L7A


title: H1bt5


title: H2med


title: H4bt5


title: C7bt5


title: H1med


title: H3bt5


title: C5bt5


title: S_cerevisiae_CEN_Rapamycin_90min

status: Public on Apr 28 2007

city: Princeton

first: Soyeon

last: Lippman

state: NJ

address: 301 Lewis Thomas Lab

institute: Princeton University

hyb_protocol: Hybridization procedure was performed as directed by Agilent’s 60-mer 11k oligo microarray processing protocol. Briefly, 400 ng each of Cy3 labeled reference sample and Cy5 labeled test sample were incubated at 60C for 17 hours with 25ul of 10x control targets. Each 400 ng sample contained more than the minimum 2.5 pmol dye incorporation. All hybridization steps were also conducted in an ozone-free facility to minimize fluorescence degradation.

scan_protocol: Arrays were washed and scanned using Agilent Technologies Scanner Model G2505B at 100 % red and green channel PMT and 10um scan resolution. Scanning software ChipScan version A.6.3.1 from Agilent was used. Scanned images were analyzed using Agilent Feature Extraction v8.1 with linear & LOWESS dye normalization and no background subtraction.

data_processing: Agilent Feature Extractor Version A.7.5.1 was used to extract the features of the scanned images. The normalized data were submitted to Princeton University MicroArray Database (PUMAdb) for analysis with the following filtering parameters: i) all flagged spots were removed; ii) all red and green population outliers were removed; iii) all red and green non-uniformity outliers were removed; iv) only spots with intensity well above background were used; and v) only genes with greater than 80 % good data for all the arrays were used for data analysis. The resultant data were analyzed using Microsoft Excel.

organism: Saccharomyces cerevisiae

label_protocol: cRNA was synthesized using Low RNA Input Linear Amplification Kit with following modifications: i) 3.25 ng of total RNA was used for cDNA synthesis; ii) 2.5ul T7 Promoter Primer was used per reaction; and iii) half the reaction volumes were used throughout the remainder of the provided protocol. The reference sample was labeled with Cyanine3-labeled CTP, and test sample was labeled with Cyanine5-labeled CTP. Amplified cRNA as well as Cy3-CTP and Cy5-CTP incorporation were quantified using NanoDrop. All steps of cRNA synthesis were conducted in an ozone-free facility to minimize fluorescence degradation.

extract_protocol: Following mechanical disruption of the cells, total RNA was extracted using RNeasy Mini Kit, including the optional DNase I step. RNA integrity was verified by gel electrophoresis. Extracted RNA was quantified using NanoDrop and diluted to 100 ng/ul with nuclease-free water.

treatment_protocol: Cells were inoculated to OD600 of 0.05 in 250ml of SC-URA using an overnight culture of cells in the same media. Cultures were grown at 30C to an OD600 of 0.05 and rapamycin was added to 100nm/ml or equal volume of drug vehicle (DMSO). Reference samples (5ml) were collected immediately prior to rapamycin addition. Test samples (5ml) were collected 20, 30, 60, 90,120 and 180 min post rapamycin treatment via vacuum filtration, transferred to liquid nitrogen then stored at -80C until RNA extraction.

tag: Strain

tag: Genotype

source_name: Cells carrying CEN plasmid 90min post [100nM] rapamycin treatment.


title: C4bt5


title: S_cerevisiae_CEN_SCH9(2D3E)_Rapamycin_180min

growth_protocol: Cells were inoculated to OD600 of 0.05 in 250ml of SC-URA using an overnight culture of cells in the same media. Cultures were grown at 30C to an OD600 of 0.05 and rapamycin was added to 100nm/ml or equal volume of drug vehicle (DMSO).

source_name: Cells carrying CEN_SCH9(2D3E) plasmid 180min post [100nM] rap treatment.


title: S_cerevisiae_CEN_SCH9(WT)_Rapamycin_60min

source_name: Cells carrying CEN_SCH9(WT) plasmid just prior to rapamycin addition

value: Mat@ ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 GAL [CEN URA3 SCH9(WT)]

source_name: Cells carrying CEN_SCH9(WT) plasmid 60min post [100nM] rap treatment.


title: S_cerevisiae_CEN_Rapamycin_60min

source_name: Cells carrying CEN plasmid just prior to rapamycin addition

source_name: Cells carrying CEN plasmid 60min post [100nM] rapamycin treatment.


title: L1B


title: S_cerevisiae_CEN_SCH9(WT)_Rapamycin_30min

source_name: Cells carrying CEN_SCH9(WT) plasmid 30min post [100nM] rap treatment.


title: S_cerevisiae_CEN_Rapamycin_180min

source_name: Cells carrying CEN plasmid 180min post [100nM] rap treatment.


title: S_cerevisiae_CEN_SCH9(2D3E)_Rapamycin_120min

source_name: Cells carrying CEN_SCH9(2D3E) plasmid just prior to rapamycin addition

source_name: Cells carrying CEN_SCH9(2D3E) plasmid 120min post [100nM] rap treatment.


title: S_cerevisiae_CEN_SCH9(2D3E)_Rapamycin_90min

source_name: Cells carrying CEN_SCH9(2D3E) plasmid 90min post [100nM] rap treatment.


title: S_cerevisiae_CEN_SCH9(WT)_Rapamycin_90min

source_name: Cells carrying CEN_SCH9(WT) plasmid 90min post [100nM] rap treatment.


title: S_cerevisiae_CEN_Rapamycin_120min

source_name: Cells carrying CEN plasmid alone 120min post [100nM] rap treatment.


title: S_cerevisiae_CEN_Rapamycin_30min

hyb_protocol: Hybridization procedure was performed as directed by Agilent’s 60-mer 11k oligo microarray processing protocol. Briefly, 400 ng each of Cy3 labeled reference sample and Cy5 labeled test sample were incubated at 60 C for 17 hours with 25 ul of 10x control targets. Each 400 ng sample contained more than the minimum 2.5 pmol dye incorporation. All hybridization steps were also conducted in an ozone-free facility to minimize fluorescence degradation.

source_name: Cells carrying CEN plasmid alone 30min post [100nM] rap treatment.


title: S_cerevisiae_CEN_SCH9(2D3E)_Rapamycin_30min

source_name: Cells carrying CEN_SCH9(2D3E) plasmid 30min post [100nM] rap treatment.


title: S_cerevisiae_CEN_SCH9(WT)_Rapamycin_180min

source_name: Cells carrying CEN_SCH9(WT) plasmid 180min post [100nM] rap treatment.


title: S_cerevisiae_CEN_Rapamycin_20min

scan_protocol: Arrays were washed and scanned using Agilent Technologies Scanner Model G2505B at 100 % red and green channel PMT and 10um scan resolution. Scanned images were analyzed using Agilent Feature Extraction v8.1 with linear & LOWESS dye normalization and no background subtraction.

extract_protocol: Following mechanical disruption of the cells, total RNA was extracted using RNeasy Mini Kit, including the optional DNase I step. RNA integrity was verified by gel electrophoresis. Extracted RNA was quantified using NanoDrop  and diluted to 100 ng/ul with nuclease-free water.

source_name: Cells carrying CEN plasmid alone 20min post [100nM] rap treatment.


title: S_cerevisiae_CEN_SCH9(WT)_Rapamycin_20min

source_name: carrying CEN_SCH9(WT) plasmid 20min post [100nM] rap treatment.


title: SF370 #4 Cy5/Cy3

status: Public on Apr 27 2007

city: New York

first: Patricia

middle: A.

last: Ryan

state: NY

address: 1230 York Ave

department: Bacterial Pathogenesis and Immunology

institute: Rockefeller University

description: Streptococci that adhere to Detroit 562 human pharyngeal cells compared to non-adherent (associated) streptococci

hyb_protocol: Labeled cDNA hybridized to array in Slide Hybridization buffer (Ambion) for 16h at 55C. Slides were then washed with 0.1x SSC.

scan_protocol: Slides scanned with Scanarray 4000 scanner (GSO Lumonics) at 10 μm per pixel resolution. Resulting images were processed using the GenePix Pro program

data_processing: Processing included probe and array quality filtering to remove probes that were saturated, displayed a low signal to noise ratio, and/or produced signal in only one dye channel. Lowess standardization performed and robust summary statistics were applied to the standardized log2-fold change data for outlier control (Huber M-estimator and unbiased MAD estimator). A Bayesian derived regularized t-test was implemented with the CyberT program for control of variance artifacts associated with low sample size.  Calculation of the P value of the log2-fold change for genes employed the Westfall-Young stepdown permutation algorithm for multiplicity adjustment in place of the Bonferroni correction.

organism: Streptococcus pyogenes

source_name: Total RNA from adherent SF370 (#4) labeled with Cy5

label_protocol: cDNA generated with random hexamers and labeled with Cy3 or Cy5 (Amersham) using Atlas labeling protocol (Clontech).

extract_protocol: Streptococci lysed with amidase enzyme lysin. RNA extracted with modified phenol-chloroform method, DNase treated and analyzed for quality.

treatment_protocol: Detroit 562 pharyngeal cell monolayers incubated with SF370 for 2.5h at 37C (MOI =100). Monolayers were then washed with PBS to recover associated (non-adherent) streptococci. Pharyngeal cells treated with modified trypsin protocol to detach adherent streptococci.

tag: adherent SF370 (#4)

source_name: Total RNA from associated SF370 (#4) labeled with Cy3

tag: associated SF370 (#4)


title: SF370 #3 Cy5/Cy3

source_name: Total RNA from adherent SF370 (#3) labeled with Cy5

tag: adherent SF370 (#3)

source_name: Total RNA from associated SF370 (#3) labeled with Cy3

tag: associated SF370 (#3)


title: SF370 #2 Cy5/Cy3

source_name: Total RNA from adherent SF370 (#2) labeled with Cy5

tag: adherent SF370 (#2)

source_name: Total RNA from associated SF370 (#2) labeled with Cy3

tag: associated SF370 (#2)


title: SF370 #3 Cy3/Cy5

source_name: Total RNA from adherent SF370 (#3) labeled with Cy3

source_name: Total RNA from associated SF370 (#3) labeled with Cy5


title: S_cerevisiae_CEN_SCH9(2D3E)_Rapamycin_20min

hyb_protocol: Hybridization procedure was performed as directed by Agilent’s 60-mer 11k oligo microarray processing protocol. Briefly, 400 ng each of Cy3 labeled reference sample and Cy5 labeled test sample were incubated at 60 C for 17 hours with 25 l of 10x control targets. Each 400 ng sample contained more than the minimum 2.5 pmol dye incorporation. All hybridization steps were also conducted in an ozone-free facility to minimize fluorescence degradation.

source_name: Cells carrying CEN_SCH9(2D3E) plasmid just prior to rapamycin addition

source_name: Cells carrying CEN_SCH9(2D3E) plasmid 20min post [100nM] rap treatment.


title: SF370 #4 Cy3/Cy5

source_name: Total RNA from adherent SF370 (#4) labeled with Cy3

source_name: Total RNA from associated SF370 (#4) labeled with Cy5


title: Exp-1 Total RNA from wildtype VRP infected L929 cells (5h)

city: Chapel Hill

first: Jennifer

last: Konopka

state: NC

address: CB 7292; 9th Floor Burnett-Womack Bldg; Manning Drive

department: Carolina Vaccine Institute

institute: University of North Carolina at Chapel Hill

description: L929 cells were mock treated or infected at an MOI of 5 with either wildtype or nt3A mutant null-VRP, and total RNA was isolated at 5 hpi using the UltraSpec reagent protocol as described above.  The UNC-CH Functional Genomics Core Facility provided Affymetrix sample preparation and hybridization services, hybridizing the samples to Affymetrix Mouse Expression 430A (MOE430A) GeneChip arrays, which include analysis of ~22,600 genes.  cDNA was synthesized using 7 ug of total RNA and a custom cDNA kit from Life Technologies using a T7-(dT)24 primer for the reaction.  Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit, and the cRNA was fragmented in fragmentation buffer (40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) at 94oC for 35 min.  15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD,  and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100 mM MES, 1M  [Na+], 20 mM EDTA, 0.01% Tween 20).  10 ug of cRNA was used for hybridization.  The arrays were hybridized for 16 h at 45oC in the GeneChip Hybridization Oven 640, followed by washing and staining with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400.  The arrays were then scanned with the Hewlett Packard GeneArray Scanner.  Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis, with sample quality assessed by examination of 3’ to 5’ intensity ratios of certain genes.  Expression analysis files created by Microarray Suite were imported into GeneSpring 6.2 (Silicon Genetics) for further gene expression analysis and filtering.  Two independent array studies were completed, and gene lists were compiled representing only those genes that were up- or downregulated by greater than 2-fold in replicate analyses.

source_name: Total RNA from wildtype null-VRP infected L929 murine fibroblast cells at 5hpi

extract_protocol: UltraSpec Reagent (Biotecx) and the manufacterer's protocol was utilized to extract total RNA from infected L929 cells.

tag: Total RNA isolated from murine L929 cells infected with wildtype null-VRP (Venezuelan equine encephalitis virus replicon particles) at 5 hrs post-infection.


title: SF370 #1 Cy3/Cy5

source_name: Total RNA from adherent SF370 (#1) labeled with Cy3

tag: adherent SF370 (#1)

source_name: Total RNA from associated SF370 (#1) labeled with Cy5

tag: associated SF370 (#1)


title: Exp-1 Total RNA from mock L929 cells (5h)

hyb_protocol: 15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD,  and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100 mM MES, 1M  [Na+], 20 mM EDTA, 0.01% Tween 20).  10 ug of cRNA was used for hybridization.  The arrays were hybridized for 16 h at 45oC in the GeneChip Hybridization Oven 640, followed by washing and staining with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400.

scan_protocol: The arrays were then scanned with the Hewlett Packard GeneArray Scanner.  Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis, with sample quality assessed by examination of 3’ to 5’ intensity ratios of certain genes.

data_processing: Expression analysis files created by Microarray Suite were imported into GeneSpring 6.2 (Silicon Genetics) for further gene expression analysis and filtering.  Two independent array studies were completed, and gene lists were compiled representing only those genes that were up- or downregulated by greater than 2-fold in replicate analyses.

source_name: Total RNA from mock treated L929 murine fibroblast cells

label_protocol: cDNA was synthesized using 7 ug of total RNA and a custom cDNA kit from Life Technologies using a T7-(dT)24 primer for the reaction.  Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit, and the cRNA was fragmented in fragmentation buffer (40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) at 94oC for 35 min.

extract_protocol: UltraSpec Reagent (Biotecx) and the manufacterer's protocol was utilized to extract total RNA from mock-infected L929 cells.


title: SF370 #1 Cy5/Cy3

source_name: Total RNA from adherent SF370 (#1) labeled with Cy5

source_name: Total RNA from associated SF370 (#1) labeled with Cy3


title: SF370 #2 Cy3/Cy5

source_name: Total RNA from adherent SF370 (#2) labeled with Cy3

source_name: Total RNA from associated SF370 (#2) labeled with Cy5


title: Exp-2 Total RNA from nt3A mutant VRP infected L929 cells (5h)

source_name: Total RNA from nt3A mutant null-VRP infected L929 murine fibroblast cells at 5hpi

tag: Total RNA isolated at 5 hrs post-infection from murine L929 cells infected with null-VRP (Venezuelan equine encephalitis virus replicon particles) containing the nt3A mutation.


title: Whole Seed at the globular stage, biological replicate 2

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Whole seeds containing globular-stage embryos were ground in liquid nitrogen using a mortar and pestle.

hyb_protocol: Following fragmentation, ten micrograms of cRNA were hybridized for 16 hr at 45¡C with the GeneChip Soybean Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating System 1.3 (GCOS 1.3) using default analysis settings and global scaling as a normalization method. The trimmed mean target intensity of each array was set to 500.

organism: Glycine max

source_name: Soybean globular stage seed

label_protocol: Two nanograms of total RNA was amplified using the RiboAmp OA Amplification Kit (Molecular Devices, Sunnyvale, CA).  Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit using all of the amplified RNA from the RiboAmp OA Kit.

growth_protocol: Soybean cv. Asgrow A3237 was grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22¡C.

extract_protocol: Total RNA was extracted using Plant RNA Isolation Reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: Seeds with globular-stage embryos were collected from pods between 7.0 and 10.0 mm in length, freezed in liquid nitrogen, and ground into powder with liquid nitrogen using a mortar and pestle.

tag: Soybean cv. Asgrow A3237


title: Whole Seed at the globular stage, biological replicate 1


title: Exp-1 Total RNA from nt3A mutant VRP infected L929 cells (5h)


title: Exp-2 Total RNA from wildtype VRP infected L929 cells (5h)


title: Isolate HOLLAND (HOLLAND_104)

type: genomic

city: Ames

first: Mike

last: Paustian

state: IA

address: 2300 Dayton Ave

institute: National Animal Disease Center, USDA-ARS

description: Comparative genomic hybridization between Map K-10 and other mycobacteria

hyb_protocol: Labeled cDNA from experimental mycobacterial isolates was purified and mixed with alternately labeled Map K10 cDNA in a final volume of 55 µL containing 3x SSC, 0.22pct SDS, and 34 µg salmon sperm DNA (Invitrogen).  This hybridization solution was incubated at 100C for 2 minutes, applied to the Map K10 microarray, and allowed to hybridize overnight at 65C.  The arrays were washed sequentially for 3 minutes at room temperature in 300 mL volumes of 0.5x SSC/0.01pct SDS, 0.5x SSC, 0.1x SSC, and 0.01x SSC, then dried by centrifugation and scanned.

scan_protocol: Microarray was scanned with a ScanArray 4000 confocal laser scanner (PerkinElmer, Boston, MA).  Laser and PMT power were adjusted to minimize pixel saturation and background fluorescence

data_processing: Raw intensity measurements for each spot on the microarray were extracted from scanned images using ScanArray Express software (PerkinElmer) and adjusted with local background subtraction and LOWESS normalization.  Poorly detected spots were removed by filtering out those in which more than 50pct of the pixels from both samples were within two standard deviations of the local background.  Note that for final analyses, triplicate spots were averaged and ORFs not represented by at least 2 replicate spots were discarded.

label: Alexa 647

molecule: genomic DNA

organism: Mycobacterium avium

label_protocol: Purified genomic DNA was randomly sheared by nebulization on ice at 10 psi for approximately 1.5 min, resulting in an average fragment size of 800 bp.  Aliquots of sheared genomic DNA (4 µg) were labeled with Invitrogen BioPrime Plus Array CGH kit.

extract_protocol: QIAGEN Genomic-tip or QIAamp DNA blood kit

tag: in vitro pure culture

label: Alexa 555

source_name: HOLLAND


title: Isolate LINDA (LINDA_101)

source_name: LINDA

label_protocol: Purified genomic DNA was randomly sheared by nebulization on ice at 10 psi for approximately 1.5 min, resulting in an average fragment size of 800 bp.  Aliquots of sheared genomic DNA (4 µg) were labeled with Invitrogen BioPrime Plus Array CGH kit


title: Isolate BEN (BEN_099)

source_name: BEN


title: Isolate 8743A (8743A_102)


title: Isolate LINDA (LINDA_100)


title: Isolate BEN (BEN_095)


title: Isolate 7297 (7297_093)


title: S_cerevisiae_CEN_SCH9(WT)_Rapamycin_120min

source_name: Cells carrying CEN_SCH9(WT) plasmid just prior to rapamycin addition

source_name: Cells carrying CEN_SCH9(WT) plasmid 120min post [100nM] rap treatment.


title: Isolate 7297 (7297_096)


title: Isolate 7896 (7896_094)


title: Isolate 7896 (7896_098)


title: Isolate MAP7 (MAP7_091)


title: Isolate MAP7 (MAP7_090)


title: Isolate MAP5 (MAP5_088)


title: Isolate MAP5 (MAP5_089)


title: Isolate 8744 (8744_092)


title: Isolate 7887 (7887_087)


title: Isolate 7926 (7926_085)


title: Isolate 8743A (8743A_103)


title: Isolate 7926 (7926_084)


title: Isolate 4137 (4137_082)


title: Isolate 7301 (7301_073)


title: Exp-2 Total RNA from mock L929 cells (5h)

tag: Total RNA from mock treated L929 murine fibroblast cells


title: Isolate MAC104 (MAC104_076)


title: Isolate 4137 (4137_083)


title: Isolate 7887 (7887_086)


title: Isolate MAC104 (MAC104_077)


title: Isolate MAC104 (MAC104_075)


title: Isolate 5001 (5001_069)


title: Isolate 4054 (4054_071)


title: Isolate 397 (397_050)


title: Isolate 397 (397_065)


title: Isolate 7565 (7565_053)


title: Isolate 4054 (4054_060)


title: Isolate 467 (467_064)


title: Isolate 5001 (5001_068)


title: Isolate 7560 (7560_052)


title: Isolate 7893 (7893_063)


title: Isolate MAP4 (MAP4_062)


title: Isolate 467 (467_051)


title: Isolate 7890 (7890_047)


title: Isolate 7876 (7876_041)


title: Isolate 7926 (7926_048)


title: Isolate 7890 (7890_045)


title: Isolate 5001 (5001_072)


title: Isolate 4137 (4137_039)


title: Isolate MAP4 (MAP4_046)


title: Isolate 7926 (7926_040)


title: Isolate 4054 (4054_038)


title: Isolate 4054 (4054_037)


title: Isolate 1018 (1018_049)


title: Isolate 7301 (7301_036)


title: Isolate 7893 (7893_043)


title: Isolate 7301 (7301_035)


title: Isolate 7876 (7876_061)


title: Isolate 7935 (7935_031)


title: Isolate 7935 (7935_030)


title: Isolate 4026 (4026_029)


title: Isolate MAP4 (MAP4_026)


title: Normospermic individual: Sample N6

city: Detroit

first: Stephen

middle: A

last: Krawetz

state: MI

address: 275 East Hancock, CS Mott Center

institute: Wayne State University

description: Spermatozoal RNA profile from a normally fertile individual

hyb_protocol: Hybridization to Illumina Sentrix Expression BeadChip, staining and washing were carried out as described (Illumina, Wallingford).

scan_protocol: Scanning procedures were carried out as described by Illumina, Wallingford.

data_processing: The data were analyzed with Illumina Beat Studio using Cubic Spline Normalization

source_name: Normal Human Spermatozoa

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA (Whole-Genome Gene Expression with IntelliHyb Seal System Manual, 2006, Illumina).

growth_protocol: Human donor

extract_protocol: Semen was collected then treated with Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100) on ice for 30 minutes.  Lack of somatic cell contamination and sperm count were established by microscopic examination.  RNA was isolated from sample using Trizol.  Samples were then treated with RNase-free DNase I.

tag: Fertility Status

value: Fertile


title: Normospermic individual: Sample N5


title: Isolate 7887 (7887_032)


title: Isolate 4137 (4137_027)


title: Normospermic individual: Sample N11


title: Teratozoospermic individual: Sample T7

description: Spermatozoal RNA profile from an infertile individual with a consistent severely teratozoospermic semen profile.

source_name: Human Sperm from an infertile male with a consistent severe heterogeneous teratozoospermia

extract_protocol: Semen was collected then treated with Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100) on ice for 30 minutes.  Lack of somatic cell contamination and sperm count were established by microscopic examination.  RNA was isolated from sample using a modified RNeasy protocol (Qiagen Inc. Valencia, CA).  RNA was eluted from collection columns using 50 microL of nuclease-free water twice for a final volume of 100 microL.  Dithiothreitol (DTT) was added to eluted samples to a final concentration of 10 mM.  A total of 40 units RNase block (Strategene, La Jolla, CA) was added to each sample prior to a 20-minute treatment with RNase-free DNase I (Ambion, Austin, TX) at 37°C.

value: Infertile


title: Isolate 7560 (7560_024)


title: Normospermic individual: Sample N12


title: Isolate 7565 (7565_025)


title: Teratozoospermic individual: Sample T3


title: Normospermic individual: Sample N1


title: Teratozoospermic individual: Sample T8


title: Teratozoospermic individual: Sample T4


title: Teratozoospermic individual: Sample T5


title: Isolate 4026 (4026_028)


title: Isolate MAP6 (MAP6_023)


title: Teratozoospermic individual: Sample T6


title: Teratozoospermic individual: Sample T2


title: Isolate 7565 (7565_016)


title: Non-pregnat endometrium (BPL_EC13B)

city: Tsukuba City

first: Koichi

last: Ushizawa

state: Ibaraki

address: Ikenodai 2

department: Animal Science Department

country: Japan

institute: National Institute of Agrobiological Sciences

description:
This data is utilized for gene expression analysis of bovine placenta.
This data is self-hybridization of Cy3 and Cy5 dyes

hyb_protocol: Before hybridization, microarray glass slides were immersed in 0.2% SDS for 2 min followed by two washes each 2 min in autoclaved Milli Q water, and subjected to blocking in 180 ml of Methyl Pyrrolidinone (Aldrich) containing 2.7 g Succinic Anhydride (Wako) and 15.3 ml 1M Boric acid (pH 8.0) solution for 20 min. Slides were then washed with autoclaved Milli Q water, and the spotted cDNA targets (microarray) were denatured in boiling water for 2 min. The slides were dehydrated in 100% ethanol for 2 min and air dried by spinning at a low speed. The mixture of labeled probes, for example, the Cy3 & Cy5, were then applied to the microarray, placed a cover slip carefully and incubated at 65C for 14 - 16 h in a custom slide chamber. After incubation for 14 - 16 h at 65C, the slides were washed in 2 x SSC / 0.01% SDS for 2 min, followed by washing in 0.2 x SSC/0.01% SDS and 0.2 x SSC, each for 2 min with gentle agitation, and air dried by spinning at a low speed.

scan_protocol: Hybridization images were immediately scanned by a GenePix 4000B laser scanner (Axon Instrument) and analyzed with GenePix Pro 4.0 computer software.

data_processing: subtracted from spot intensity data. The subtracted intensity data were subjected to global normalization.

organism: Bos taurus

source_name: Non-pregnat endometrium

label_protocol: Two-microgram of pooled polyA+ RNA of tissue obtained from pregnant cows was reverse transcribed in the presence of cyanine-3-fluorescent (Cy3) and dyecyanine-5-fluorescent dye (Cy5)-conjugated dUTP (Amersham Bioscience) by using Superscript II reverse transcriptase (Invitrogen) to yield Cy3 and  Cy5 fluorescence-labeled cDNA probe. After a 2-h reverse transcription reaction at 42C, RNA was degraded by addition of 1.5 micro-l of an alkaline solution (1N NaOH / 20 mM EDTA), and neutralized by addition of 1.5 micro-l 1N HCl.The Cy3 and Cy5 cDNA probe were then mixed and washed by centrifugation with TE (Tris-EDTA, pH 7.0) first and then with TE, 20 micro-g Salmon sperm DNA, 20 micro-g polyA and 20 micro-g yeast RNA in a Microcon YM-30 column (Millipore). The concentrated probe mix was adjusted with TE to a volume of 10 micro-l, denatured at 100C for 2 min, spun for a few min and made to a final hybridization volume of 15 micro-l with 2.55 micro-l 20XSSC and 0.45 micro-l 10% SDS and kept at room temperature until used.

extract_protocol: Total RNA was isolated from the samples using ISOGEN (NipponGene) according to the manufacturer's instructions.  PolyA RNA was isolated from the samples using Oligotex-dT30 Super (Roche) according to the manufacturer's instructions.

tag: Bovine endometrium of estrus cycle day13

tag: Sample B


title: Teratozoospermic individual: Sample T1


title: Isolate MAP6 (MAP6_010)


title: Isolate 1018 (1018_014)


title: Isolate 7889 (7889_011)


title: Non-pregnat endometrium (BPL_EC13A)

tag: Sample A


title: Isolate 1018 (1018_009)


title: Day 250 caruncle and cotyledon (BPL_250B1)

description: This data is utilized for gene expression analysis of bovine placenta.

source_name: Day250 cotyledon

label_protocol: Two-microgram of pooled polyA+ RNA of tissue obtained from pregnant cows was reverse transcribed in the presence of cyanine-5-fluorescent dye (Cy5)-conjugated dUTP (Amersham Bioscience) by using Superscript II reverse transcriptase (Invitrogen) to yield Cy5 fluorescence-labeled cDNA probe. After a 2-h reverse transcription reaction at 42C, RNA was degraded by addition of 1.5 micro-l of an alkaline solution (1N NaOH / 20 mM EDTA), and neutralized by addition of 1.5 micro-l 1N HCl.The Cy5 cDNA probe were then mixed and washed by centrifugation with TE (Tris-EDTA, pH 7.0) first and then with TE, 20 micro-g Salmon sperm DNA, 20 micro-g polyA and 20 micro-g yeast RNA in a Microcon YM-30 column (Millipore). The concentrated probe mix was adjusted with TE to a volume of 10 micro-l, denatured at 100C for 2 min, spun for a few min and made to a final hybridization volume of 15 micro-l with 2.55 micro-l 20XSSC and 0.45 micro-l 10% SDS and kept at room temperature until used.

tag: Bovine cotyledon of day 250 of gestation

source_name: Day250 caruncle

label_protocol: Two-microgram of pooled polyA+ RNA of tissue obtained from pregnant cows was reverse transcribed in the presence of cyanine-3-fluorescent dye (Cy3)-conjugated dUTP (Amersham Bioscience) by using Superscript II reverse transcriptase (Invitrogen) to yield Cy3 fluorescence-labeled cDNA probe. After a 2-h reverse transcription reaction at 42C, RNA was degraded by addition of 1.5 micro-l of an alkaline solution (1N NaOH / 20 mM EDTA), and neutralized by addition of 1.5 micro-l 1N HCl.The Cy3 cDNA probe were then mixed and washed by centrifugation with TE (Tris-EDTA, pH 7.0) first and then with TE, 20 micro-g Salmon sperm DNA, 20 micro-g polyA and 20 micro-g yeast RNA in a Microcon YM-30 column (Millipore). The concentrated probe mix was adjusted with TE to a volume of 10 micro-l, denatured at 100C for 2 min, spun for a few min and made to a final hybridization volume of 15 micro-l with 2.55 micro-l 20XSSC and 0.45 micro-l 10% SDS and kept at room temperature until used.

tag: Bovine caruncle of day 250 of gestation


title: Day 150 caruncle and cotyledon (BPL_150B1)

source_name: Day150 cotyledon

tag: Bovine cotyledon of day 150 of gestation

source_name: Day150 caruncle

tag: Bovine caruncle of day 150 of gestation


title: Day 250 caruncle and cotyledon (BPL_250A1)


title: Day 250 caruncle and cotyledon (BPL_250A2)


title: Isolate 7889 (7889_012)


title: Day 150 caruncle and cotyledon (BPL_150B2)


title: Day 150 caruncle and cotyledon (BPL_150A1)


title: Isolate 467 (467_002)


title: Isolate 6058 (6058_230)


title: Isolate 467 (467_006)


title: Day 150 caruncle and cotyledon (BPL_150A2)


title: Isolate 9040 (9040_229)


title: Isolate 7560 (7560_004)


title: Isolate 7565 (7565_008)


title: Isolate 397 (397_226)


title: Day 60 caruncle and cotyledon (BPL_60B2)

source_name: Day60 caruncle

tag: Bovine caruncle of day 60 of gestation

source_name: Day60 cotyledon

tag: Bovine cotyledon of day 60 of gestation


title: Day 60 caruncle and cotyledon (BPL_60A1)


title: Isolate 9034 (9034_228)


title: Isolate 9034 (9034_227)


title: Day 25 extra-embryonic membrane and endometrium (BPL_25A2)

source_name: Day25 endometrium

tag: Bovine endometrium of day 25 of gestation

source_name: Day25 extra-embryonic membrane

tag: Bovine extra-embryonic membrane of day 25 of gestation


title: Day 60 caruncle and cotyledon (BPL_60A2)

source_name: Day 60 Caruncle

source_name: Day60 Cotyledon


title: Day 25 extra-embryonic membrane and endometrium (BPL_25B1)


title: Isolate 397 (397_220)


title: Isolate 6007 (6007_232)


title: Isolate 397 (397_225)


title: Isolate 397 (397_219)


title: Day 60 caruncle and cotyledon (BPL_60B1)


title: Day 25 extra-embryonic membrane and endometrium (BPL_25B2)

source_name: Day 25 extra-embryonic membrane


title: Isolate 6007 (6007_218)


title: Isolate M.silv.attcc (M.silv.attcc_217)


title: Isolate 6071 (6071_216#2)


title: Day 25 extra-embryonic membrane and endometrium (BPL_25A1)

source_name: Day 25 endometrium


title: Isolate 397 (397_007)


title: Isolate 9040 (9040_231)


title: Isolate 6071 (6071_215)


title: Isolate 6057 (6057_212)


title: SJL/J_male_hypothalamus

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: standard Affymetrix procedures except for custom GNF array washer

scan_protocol: standard Affymetrix procedures using the GeneChip 3000 scanner

label_protocol: cDNA synthesis and amplification employed the Affymetrix 3' IVT protocol.

extract_protocol: Hypothalamus tissue was harvested from 32 strains of mice from the Mouse Diversity Panel.  Total RNA was isolated from frozen tissue using Trizol, and cleaned up using an RNeasy kit (Qiagen).  One microgram total RNA from three separate samples was pooled and 3 ug used for cDNA synthesis and amplification.


title: SPRET/EiJ_male_hypothalamus


title: SWR/J_male_hypothalamus


title: Isolate 6057 (6057_213)


title: RIIS/J_male_hypothalamus


title: WSB/EiJ_male_hypothalamus


title: SEA/GnJ_male_hypothalamus


title: SM/J_male_hypothalamus


title: Isolate 6049 (6049_207)


title: Isolate 6052 (6052_211)


title: PERA/EiJ_male_hypothalamus


title: Isolate M.silv.attcc (M.silv.attcc_214)


title: NOD/LtJ_male_hypothalamus


title: Isolate 6054 (6054_209)


title: Isolate 6006 (6006_208)


title: PWK/Ph_male_hypothalamus


title: MOLF/EiJ_male_hypothalamus


title: MSM/Ms_male_hypothalamus


title: NZW/LacJ_male_hypothalamus


title: Isolate 6058 (6058_176)


title: Isolate 7935 (7935_162)


title: PL/J_male_hypothalamus


title: Isolate 6054 (6054_204)


title: Isolate 6049 (6049_179)


title: Isolate 6006 (6006_203)


title: Isolate 6052 (6052_210)


title: JF1/Ms_male_hypothalamus


title: FVB/NJ_male_hypothalamus


title: Isolate 7887 (7887_161)


title: CBA/J_male_hypothalamus


title: MA/MyJ_male_hypothalamus


title: Isolate 467 (467_159)


title: Isolate 7265 (7265_156)


title: I/LnJ_male_hypothalamus


title: NZB/BINJ_male_hypothalamus


title: C57L/J_male_hypothalamus


title: Isolate 7265 (7265_160)


title: C57BLKS/J_male_hypothalamus


title: Day 250 caruncle and cotyledon (BPL_250B2)


title: DBA/2J_male_hypothalamus


title: CAST/EiJ_male_hypothalamus


title: Isolate 7301 (7301_142)


title: C57BL/6J_male_hypothalamus


title: Isolate MAP5 (MAP5_143)


title: Isolate 9040 (9040_141)


title: C3H/HeJmale_hypothalamus


title: Isolate 5001 (5001_144)


title: C57BL/10Jmale_hypothalamus


title: CZECHII/EiJ_male_hypothalamus


title: Isolate 7265 (7265_140)


title: Isolate 7301 (7301_157)


title: Isolate 7935 (7935_136)


title: Isolate K10 (K10_134)


title: Isolate 7265 (7265_135)


title: A/J_male_hypothalamus


title: Isolate 4054 (4054_139)


title: Isolate 7893 (7893_137)


title: BALB/cByJ_male_hypothalamus


title: BTBR T+ tf/J_male_hypothalamus

description: BTBR T+ tf/J_male_hypothalamus

source_name: BTBR T+ tf/J_male_hypothalamus

tag: BTBR T+ tf/J_male_hypothalamus


title: Isolate 5001 (5001_138)


title: Isolate 7301 (7301_158)


title: AKR/J_male_hypothalamus


title: 129S1/SvImJ_male_hypothalamus


title: Isolate 9040 (9040_133)


title: BUB/BnJmale_hypothalamus


title: Isolate 9040 (9040_132)


title: Normospermic individual: Sample 23G

description: Spermatozoal RNA profile a fertile individual

source_name: Human Sperm from a fertile male

extract_protocol: Semen was collected then treated with Somatic Cell Lysis Buffer (0.1% sodium  dodecyl sulfate [SDS], 0.5% Triton X-100) on ice for 30 minutes.  Lack of somatic cell contamination and sperm  count were established by microscopic examination.  Samples were lysed and RNAs stabilized in a chaotropic buffer.  RNA was isolated from sample using a modified RNeasy  protocol (Qiagen Inc. Valencia, CA).  RNA was eluted from collection columns using 50 microL of nuclease-free  water twice for a final volume of 100 microL.  Dithiothreitol (DTT) was added to eluted samples to a final  concentration of 10 mM.  A total of 40 units RNase block (Strategene, La Jolla, CA) was added to each sample  prior to a 20-minute treatment with RNase-free DNase I (Ambion, Austin, TX) at 37°C.


title: Isolate 9034 (9034_130)


title: Isolate 9034 (9034_131)


title: Normospermic individual: Sample 23H


title: Isolate 7297 (7297_128)


title: Normospermic individual: Sample 19C


title: Isolate 397 (397_129)


title: Normospermic individual: Sample 19B


title: Laser capture microdissected (LCM) suspensor at the globular stage, biological replicate 1 (SRB)

description: Suspensor regions from globular embryos were microdissected using the LEICA AS LMD system.

hyb_protocol: Following fragmentation, nine micrograms of cRNA were hybridized for 16 hr at 45°C with the GeneChip Soybean Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

organism: Phaseolus coccineus

source_name: SRB globular stage suspensor captured by LCM

label_protocol: Approximately 106 ng of total RNA was amplified using the MessageAmp II Kit (Ambion, Austin, TX) and SMART III primer (Clontech).  Approximately 200 ng of cDNA derived from the amplified RNA was used for biotinylated cRNA synthesis using the ENZO BioArray High Yield RNA Transcript Labeling Kit.

growth_protocol: SRB cv. Hammond's Dwarf Red Flower was grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22°C.

extract_protocol: Total RNA was extracted using the PicoPure RNA Extraction Kit (Molecular Devices, Sunnyvale, CA).

treatment_protocol: Flowers were hand-pollinated and tagged.  Six days after pollination, seeds containing globular-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Embryo region was captured from six-micron sections using a Leica AS LMD System.

tag: SRB cv. Hammond's Dwarf Red Flowers


title: Laser capture microdissected (LCM) suspensor at the globular stage, biological replicate 2 (SRB)

label_protocol: Approximately 137 ng of total RNA was amplified using the MessageAmp II Kit (Ambion, Austin, TX) and SMART III primer (Clontech).  Approximately 200 ng of cDNA derived from the amplified RNA was used for biotinylated cRNA synthesis using the ENZO BioArray High Yield RNA Transcript Labeling Kit.


title: Teratozoospermic individual: Sample 23E

source_name: Human Sperm from an infertile male with a consistent severe teratozoospermia


title: Teratozoospermic individual: Sample 23C


title: Isolate MAA104 (MAA104_127)


title: Isolate 7896 (7896_125)


title: Isolate MAP5 (MAP5_122)


title: Isolate MAP3 (MAP3_121)


title: Isolate 7301 (7301_126)


title: Teratozoospermic individual: Sample 23B


title: Isolate MAP3 (MAP3_123)


title: Teratozoospermic individual: Sample 23D


title: Teratozoospermic individual: Sample 23A


title: Teratozoospermic individual: Sample 23F


title: abnormal eye & brain gene expression patterns in homozygous mbl/axin1 zebrafish - mbl 72hpf-B

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

hyb_protocol: The labeled cDNA was added to ChipHybeTM hybridization buffer (Ventana Medical Systems, Tucson) containing Cot-1 DNA (0.5 mg/ml), yeast tRNA (0.2 mg/ml), and poly(dA)40-60 (0.4 mg/ml).  Hybridization was performed on a Ventana Discovery system for 9 hr at 58C

scan_protocol: Agilent DNA Microarray Scanner Model G2505B with fluorescent intensity was measured by Imagene™ software

data_processing: method of Dozmorov & Centola, Bioinformatics 19:204-211, 2003.

organism: Danio rerio

source_name: mbl/mbl 72 hr post-fertilization RNA replicate 2

label_protocol: Direct labeling incorporating Cy3-dUTP in cDNA from 2 micrograms total RNA with anchored oligo-dT priming and Omniscript reverse transcriptase

extract_protocol: Trizol

treatment_protocol: Total RNA was obtained from approximately 50 embryos or larvae 72 hours post-fertilization

tag: RNA obtained from mbl/mbl zebrafish embryos 72 hours post fertilization


title: Laser capture microdissected (LCM) embryo proper at the globular stage, biological replicate 1 (SRB)

description: Embryo proper regions from globular embryos were microdissected using the LEICA AS LMD system.

source_name: SRB globular stage embryo proper captured by LCM

label_protocol: Approximately 60 ng of total RNA was amplified using the MessageAmp II Kit (Ambion, Austin, TX) and SMART III primer (Clontech).  Approximately 200 ng of cDNA derived from the amplified RNA was used for biotinylated cRNA synthesis using the ENZO BioArray High Yield RNA Transcript Labeling Kit.


title: Laser capture microdissected (LCM) embryo proper at the globular stage, biological replicate 2 (SRB)

label_protocol: Approximately 75 ng of total RNA was amplified using the MessageAmp II Kit (Ambion, Austin, TX) and SMART III primer (Clontech).  Approximately 200 ng of cDNA derived from the amplified RNA was used for biotinylated cRNA synthesis using the ENZO BioArray High Yield RNA Transcript Labeling Kit.


title: abnormal eye & brain gene expression patterns in homozygous mbl/axin1 zebrafish - mbl 72hpf-A

source_name: mbl/mbl 72 hr post-fertilization RNA replicate 1

treatment_protocol: Total RNA was obtained from approximately 50 embryos or larvae 24 hours post-fertilization


title: Isolate Ben (Ben_118)

tag: in vitro pure culture

source_name: Ben


title: abnormal eye & brain gene expression patterns in homozygous mbl/axin1 zebrafish - mbl 48hpf-B

source_name: mbl/mbl 48 hr post-fertilization RNA replicate 2

tag: RNA obtained from mbl/mbl zebrafish embryos 48 hours post fertilization


title: abnormal eye & brain gene expression patterns in homozygous mbl/axin1 zebrafish - mbl 24hpf-B

source_name: mbl/mbl 24 hr post-fertilization RNA replicate 2

tag: RNA obtained from mbl/mbl zebrafish embryos 24 hours post fertilization


title: Isolate MAP7 (MAP7_119)


title: abnormal eye & brain gene expression patterns in homozygous mbl/axin1 zebrafish - mbl 48hpf-A

source_name: mbl/mbl 48 hr post-fertilization RNA replicate 1


title: Isolate LINDA (LINDA_117)

source_name: LINDA


title: Isolate 7288 (7288_115)


title: Isolate 7288 (7288_116)


title: Isolate 8744A (8744A_114)


title: abnormal eye & brain gene expression patterns in homozygous mbl/axin1 zebrafish - wild-type 72hpf-B

source_name: wild-type 72 hr post-fertilization RNA replicate 2

tag: RNA obtained from wild-type zebrafish embryos 72 hours post fertilization


title: Isolate HOLLAND (HOLLAND_120)

source_name: HOLLAND


title: abnormal eye & brain gene expression patterns in homozygous mbl/axin1 zebrafish - wild-type 72hpf-A

source_name: wild-type 72 hr post-fertilization RNA replicate 1


title: abnormal eye & brain gene expression patterns in homozygous mbl/axin1 zebrafish - mbl 24hpf-A

source_name: mbl/mbl 24 hr post-fertilization RNA replicate 1


title: abnormal eye & brain gene expression patterns in homozygous mbl/axin1 zebrafish - wild-type 48hpf-A

source_name: wild-type 48 hr post-fertilization RNA replicate 1

treatment_protocol: Total RNA was obtained from approximately 50 embryos or larvae 48 hours post-fertilization

tag: RNA obtained from wild-type zebrafish embryos 48 hours post fertilization


title: abnormal eye & brain gene expression patterns in homozygous mbl/axin1 zebrafish - wild-type 24hpf-B

source_name: wild-type 24 hr post-fertilization RNA replicate 2

tag: RNA obtained from wild-type zebrafish embryos 24 hours post fertilization


title: Isolate 8744 (8744_111)


title: Isolate 8744A (8744A_113)


title: Isolate HOLLAND (HOLLAND_105)


title: Isolate MAP3 (MAP3_106)


title: EHEC LB 7 h 7HI biofilm cells

status: Public on Apr 26 2007

city: College Station

first: Jintae

last: Lee

department: Chemical Engineering

institute: Texas A&M University

description: RNA extracted from biofilm cells of EHEC wild type after 7h of growth in LB and 1000 micro M 7-hydroxyindole with glass wool

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli antisense array at 45°C for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

scan_protocol: The microarray was scanned at 570 nm to get an image file by the GeneChip Scanner 3000 (Affymetrix).  Using GeneChip® Operating Software, total cell intensity was scaled automatically in the software to an average value of 500.

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: 7 h 7HI biofilm cells

label_protocol: The total RNA samples were first converted into cDNA through a reverse transcription reaction with poly-A RNA controls spiked into the same reaction mixture to monitor the entire target labeling process.  The cDNA was then digested with DNase I (Amersham Biosciences) to produce 50-200 bp fragments, which was checked by running the fragmented cDNA on a 2% agarose gel.  The fragmented cDNA was labeled at the 3’ termini by the Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP (Affymetrix, P/N 900181).

extract_protocol: To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia/silica beads (Biospec) were added to the frozen bead beater tubes containing the cell pellets. The tubes were closed tightly and beat for 50 seconds at the maximum speed in a mini bead beater (cat. no. 3110BX, Biospec). The total RNA was isolated by following the protocol of the RNeasy Mini Kit (Qiagen) including an on-column DNase digestion with RNase-free DNase I (Qiagen).


title: abnormal eye & brain gene expression patterns in homozygous mbl/axin1 zebrafish - wild-type 24hpf-A

hyb_protocol: The labeled cDNA was added to ChipHybeTM hybridization buffer (Ventana Medical Systems, Tucson) containing Cot-1 DNA (0.5 mg/ml), yeast tRNA (0.2 mg/ml), and poly(dA)40-60 (0.4 mg/ml).  Hybridization was performed on a Ventana Discovery system for 9 hr at 58 0C

source_name: wild-type 24 hr post-fertilization RNA replicate 1


title: EHEC LB 7 h isatin biofilm cells

description: RNA extracted from biofilm cells of EHEC wild type after 7h of growth in LB and 250 micro M isatin with glass wool

source_name: 7 h isatin biofilm cells


title: EHEC LB 7 h suspension cells

description: RNA extracted from suspension cells of EHEC wild type after 7 h of growth in LB and 0.1 % DMF with glass wool

source_name: 7 h suspension cells


title: abnormal eye & brain gene expression patterns in homozygous mbl/axin1 zebrafish - wild-type 48hpf-B

source_name: wild-type 48 hr post-fertilization RNA replicate 2


title: MYB51_OE_rep2

city: Rehovot

first: Eyal

last: Blum

address: P.O. Box 26

department: Plant

country: Israel

institute: Weizmann Institute of Science

description: In most angiosperms, polarity of leaves in the adaxial-abaxial sides could be associated with differences in morphology and anatomy that reflect the function of either side surfaces. Since dissecting these two parts is technically difficult, examples of metabolic pathways activated in one side of leaves and not in the other are scarce. In this study we used a developmental genetic approach to elucidate the molecular machinery that controls polarity in Arabidopsis leaves. One significant outcome of this strategy was the discovery that expression of three R2-R3 MYB factors, controlling a major pathway of secondary metabolism in Arabidopsis, was localized to the abaxial regions of young leaves. Herein we present in planta evidence that these three genes together with a second group of genes that includes the previously described ATR1 factor and its closest homolog, play a critical role in the transcriptional control of the biosynthetic pathways leading to the formation of the two most prominent classes of GSs in Arabidopsis. Silencing of either one of these two groups of genes using synthetic microRNAs resulted in reduced levels of GSs in leaves. Overexpression of the MYB28-like clade members (MYB28, MYB29 and MYB76) and the ATR1-like members [MYB51, MYB34 (ATR1)] in Arabidopsis led to induction of gene expression and metabolism associated with aliphatic glucosinolates (AGs) and indole glucosinolates (IGs), respectively. At the same time, overexpression of either clade members suppressed expression and metabolism associated with the other pathway, signifying a reciprocal, negative feedback control in between the two GSs pathways. Furthermore, we found that both members of the ATR1-like clade were not only key controllers of IGs homeostasis, but also effected metabolism of auxin and the phytoalexin camalexin. The availability of plants producing high levels of either IGs or AGs allowed us to compare between the capacities of these two types of GSs to deter herbivory. The results demonstrated that AGs exhibit more potent deterrent properties against the whitefly, Bemisia tabaci, a major agricultural pest of field and horticultural crops. Taken as a whole, this work provides a framework for dissecting the spatial regulation of metabolic pathways associated with secondary metabolism and its co-evolution with insect behavior.

hyb_protocol: Labeled cRNA was prepared and hybridized to Affymetrix ATH1 GeneChips, according to the manufacturer's guidelines (Affymetrix, Santa Clara, CA)

organism: Arabidopsis thaliana

source_name: MYB51 OE 14 day seedling

growth_protocol: Arabidopsis seedlings were grown in short day conditions (10h L/14h D, 20°C). These conditions were applied in order to prevent the plant from entering the reproductive stage. Using micro scissors, plants were collected from 14 days old whose cotyledons and hypocotyls were removed.

extract_protocol: Total RNA (15 μg) was extracted with the RNeasy RNA isolation kit (Qiagen).

tag: 14 day seedling


title: EHEC LB 7 h biofilm cells

description: RNA extracted from biofilm cells of EHEC wild type after 7 h of growth in LB and 0.1 % DMF with glass wool

source_name: 7 h biofilm cells

tag: RNA extracted from biofilm cells of EHEC wild type after 7h of growth in LB and 0.1 % DMF with glass wool


title: Laser capture microdissected (LCM) outer integument at the globular stage, biological replicate 3

description: Outer integument regions from globular stage seeds were microdissected using the LEICA AS LMD system.

hyb_protocol: Following fragmentation, Ten micrograms of cRNA were hybridized for 16 hr at 45?C with the GeneChip Soybean Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

source_name: Soybean globular stage outer integument captured by LCM

label_protocol: Eight nanograms of total RNA was amplified using the RiboAmp OA Amplification Kit (Molecular Devices, Sunnyvale, CA).  Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit using all of the amplified RNA from the RiboAmp OA Kit.

growth_protocol: Soybean cv. Asgrow A3237 was grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22?C.

treatment_protocol: Pods with lengths between 0.5 and 1.2 cm containing seeds with globular-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from six-micron sections using a Leica AS LMD System.

tag: Soybean cv. Asgrow A3237


title: Laser capture microdissected (LCM) hilum at the globular stage, biological replicate 1

description: Hilum regions from globular stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean globular stage hilum captured by LCM


title: Laser capture microdissected (LCM) hilum at the globular stage, biological replicate 2


title: Laser capture microdissected (LCM) epidermis at the globular stage, biological replicate 3

description: Epidermis regions from globular stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean globular stage epidermis captured by LCM


title: Laser capture microdissected (LCM) outer integument at the globular stage, biological replicate 2


title: Laser capture microdissected (LCM) hilum at the globular stage, biological replicate 3


title: Laser capture microdissected (LCM) inner integument at the globular stage, biological replicate 1

description: Inner integument regions from globular stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean globular stage inner integument captured by LCM


title: Laser capture microdissected (LCM) endothelium at the globular stage, biological replicate 1

description: Endothelium regions from globular stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean globular stage endothelium captured by LCM


title: Laser capture microdissected (LCM) inner integument at the globular stage, biological replicate 2


title: Laser capture microdissected (LCM) inner integument at the globular stage, biological replicate 3


title: Laser capture microdissected (LCM) outer integument at the globular stage, biological replicate 1


title: Isolate 8744 (8744_112)

description: Comparative genomic hybridization between Map K-10 and other mycobacteria


title: Laser capture microdissected (LCM) endosperm at the globular stage, biological replicate 2

description: Endosperm regions from globular stage seeds were microdissected using the LEICA AS LMD system.

source_name: Soybean globular stage endosperm captured by LCM


title: Laser capture microdissected (LCM) epidermis at the globular stage, biological replicate 1


title: Laser capture microdissected (LCM) endosperm at the globular stage, biological replicate 1