title: Azaspiracid (1nM)_Jurkat_24 hr_array #105_+

status: Public on Feb 19 2008

city: Charleston

first: Mike

last: Twiner

state: SC

address: 219 Fort Johnson Rd

department: Marine Biotoxins

institute: NOAA/NOS

description: 24 hr exposure; 1 nM AZA-1

hyb_protocol: Microarrays were imaged using an Agilent microarray scanner. Images were extracted with Agilent Feature Extraction software version A7.5.1 and data analyzed with the Rosetta Resolver 7.0 gene expression analysis system (Rosetta Informatics, Seattle, WA, USA). Using a rank consistency filter, features were subjected to a combination linear and LOWESS normalization algorithm (www.agilent.com). Based on the Rosetta error model designed for the Agilent platform, a composite array was generated at each time point, in which the data for each feature underwent a weighted averaging based on feature quality in the triplicate arrays making up the composite.

scan_protocol: Arrays were scanned with an Agilent microarray scanner at a 10 um scan resolution. Scans were with both the red and green PMT concurrently. Adjustments were made to the PMT intensity as necessary.

data_processing: Agilent Feature Extraction 7.5.1

source_name: Jurkat cells exposed to MeOH (o.1% v/v)

label_protocol: Four hundred nanograms of total RNA from each time-matched control and treatment sample were amplified separately and labeled with either Cy3 or Cy5 conjugated CTP (Perkin Elmer, Boston, MA, USA) with a low input linear amplification kit (Agilent Technologies, Palo Alto, CA, USA) according to manufacturer’s protocol. After labeling and clean up, amplified RNA was quantified by UV-vis spectroscopy. One microgram each of Cy3- and Cy5-labeled targets were combined and hybridized to an Agilent whole human genome oligonucleotide microarray (cat.# G4112A) array for 17 hr at 60°C. After hybridization, arrays were washed consecutively in solutions of 6X SSPE with 0.005% N-lauroylsarcosine and 0.06X SSPE with 0.005% N-lauroylsarcosine for 1 minute each at room temperature, followed by a 30 s rinse in Agilent stabilization and drying solution. Biological replicates, including a dye swap, were performed at each time point.

growth_protocol: Human Jurkat E6-1 lymphocyte T cells (American Type Culture Collection #TIB-152; Manassas, VA, USA) were grown in RPMI medium supplemented with 10% (v/v) fetal bovine serum (FBS) and maintained in humidified 5%:95% CO2:air at 37 oC. Cells were subcultured every 5 to 7 days with fresh medium by transferring 1 ml of cells to 9 ml of fresh supplemented medium in 75 cm^2 screw cap culture flasks.

extract_protocol: Immediately following centrifugation at 1000 x g for 5 min, cells were disrupted by resuspending in 1 ml Tri-Reagent (Molecular Research Center, Inc., Cincinnati, OH, USA). All samples were processed according to manufacturer?s protocol. Total RNA was resuspended in DEPC water, purified with a Qiagen RNeasy column (Valencia, CA, USA), and quantified by UV-vis spectroscopy. The RNA was then qualified on an Agilent 2100 Bioanalyzer (Palo Alto, CA, USA) to confirm the yield of high quality RNA.

treatment_protocol: For each experimental replicate (n = 3), 60 ml of cell culture were centrifuged at 1000 x g for 7 min and resuspended in 40 ml of fresh RPMI medium supplemented with FBS. Freshly resuspended cells were inoculated into 35 mm Petri dishes containing 2 ml total volume. Total cell numbers per dish ranged between 4.4 and 10.6 x 106 cells for the biological replicates at each time point. Cells were grown for >12 hr prior to addition of AZA-1 (1 nM final) or equivalent amounts of methanolic vehicle (0.1% final) in order to allow recovery from any stress induced by centrifugation. The cells were harvested for RNA extractions at 24 hr.

tag: Human Jurkat E6-1 lymphocyte T cells (ATCC# TIB-152)

source_name: Jurkat cells exposed to azaspiracid (1 nM)

treatment_protocol: For each experimental replicate (n = 3), 60 ml of cell culture were centrifuged at 1000 x g for 7 min and resuspended in 40 ml of fresh RPMI medium supplemented with FBS. Freshly resuspended cells were inoculated into 35 mm Petri dishes containing 2 ml total volume. Total cell numbers per dish ranged between 4.4 and 10.6 x 106 cells for the biological replicates at each time point. Cells were grown for >12 hr prior to addition of AZA-1 (10 nM final; 3-fold the 24 hr EC50; Twiner et al. (2005)) or equivalent amounts of methanolic vehicle (0.1% final) in order to allow recovery from any stress induced by centrifugation. The cells were harvested for RNA extractions at 1, 4, and 24 hr.


title: M2a - htrA_MDS

status: Public on Feb 01 2008

type: RNA

city: Gainesville

first: Paulo

last: Rodrigues

state: FL

address: 1600 Archer Rd

department: Oral Biology

country: USA

institute: University of Florida

description: Biological replicate 2 of 4. htrA mutant cells, untreated, harvested at late-log growth phase.

hyb_protocol: Four individual Cy3-labeled cDNA samples originating from four different cultures of W83 or W830593 grown in broth without antibiotics, were hybridized to the arrays along with Cy5-labeled reference cDNA samples, for a total of 8 slides.  Hybridizations were carried out in a MAUI 4-bay hybridization system (BioMicro Systems) for 16 h at 42ºC.

scan_protocol: GenePix scanner (Axon) at 532 nm (Cy3 channel) and 635 nm (Cy5 channel) with a Cy3:Cy5 ratio of 1:1.

data_processing: 16-bit TIFF single-channel images were stored and later loaded into TIGR Spotfinder software (http://www.tm4.org/spotfinder.html). The intensity values of each spot were measured and then normalized using LOWESS (LocFit Normalization – mode: global) and Interlog Mean (Interactive Log Mean Centering Normalization) using the default settings, but with the following modification: one bad channel tolerance: generous; followed by in-slide replicate analysis using TIGR MIDAS software (http://www.tm4.org/midas.html). Spots that were flagged as faulty, due to either low intensity values or signal saturation, were automatically discarded. Final statistical analysis was carried out using BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html). A total of 1902 genes passed the filtering criteria after the analysis by the BRB software. Class prediction was then, determined at p value of 0.005.

molecule: total RNA

organism: Porphyromonas gingivalis

source_name: Total RNA from htrA mutant labeled with Cyanine-3 (green)

label_protocol: Reverse transcription reactions were performed according to the protocol provided by The Institute of Genomic Research (TIGR) at http://pfgrc.tigr.org/protocols.shtml with the following minor modifications: Superscript III (Invitrogen) was used as the reverse transcriptase, the amount of RNA used was increased to 5.0 µg, and the molar ratio of aa-dUTP:dTTP used was 2:1. Purified W83 and LY2003 cDNAs were then, coupled with Cy3, while reference cDNAs were coupled with Cy5

growth_protocol: P. gingivalis wild type W83 and strain W830593 were grown in 40 ml of TSB to an optical density of 2.0 at 600 nm

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

tag: htrA mutant strain W83

source_name: Total RNA isolated from W83 cells grown in TSB to an optical density of 0.5, 1.0, 1.5 and 2.0 at 600 nm, pooled and labeled with Cyanine-5 (green).

tag: strain W83


title: Azaspiracid_jurkat_4 hr_array #146_+

description: 4 hr exposure

organism: Homo sapiens

source_name: Jurkat cells exposed to azaspiracid (10 nM)


title: M1a - htrA_MDS

description: Biological replicate 1 of 4. htrA mutant cells, untreated, harvested at late-log growth phase.


title: Azaspiracid_Jurkat_24 hr_array #104_+

description: 24 hr exposure

source_name: Jurkat cells exposed to MeOH (0.1% v/v)

source_name: Jurkat cells exposed to 10nM AZA-1


title: 04-24R-rep1

status: Public on Jan 31 2008

city: Chicago

first: Pan

last: Du

state: IL

address: 676 N ST Clair St, 1200#

institute: Northwestern University

description:
04-24R a
African American with glaucoma

hyb_protocol: Purified biotin-labeled cRNA was fragmented before the hybridization. Hybridization of the labeled cRNA to Human Genome U133A 2.0 and U95 chips (Affymetrix, Santa Clara, CA) was carried out by using Genechip Instrument System (Affymetrix) at the Genechip Core Facility of Washington University (Saint Louis, MO).

scan_protocol: The arrays were washed and stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR) followed by scanning on an Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA), and then scanned by an Affymetrix Genearray Scanner.

data_processing: RMA normalized using affy Bioconductor package

label: biotin

source_name: Human optic nerve head astrocytes, glaucoma

label_protocol: cRNA was synthesized from 2-5 µg purified RNA by using Superscript Choice system (Gibco BRL Life Technologies, Gaithersburg, MD ) and  T7-(dT)24 primer (GENSET, La Jolla, CA). Using Bioassay High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY), in vitro transcription was carried out by using the cleaned double-stranded cDNA as a template in the presence of biotinylated UTP and CTP.

growth_protocol: Four explants from each lamina cribrosa were dissected and placed into 25-cm2 Primaria tissue culture flasks and maintained in DMEM-F12 supplemented with 10% FBS and antibiotics.Cells were kept in a 37oC, 5% CO2 incubator. After 2-4 weeks, primary cultures were purified by using modified immunopanning procedure described by Mi and Barres (1999). Purified cells were expanded after characterization by immunostaining for astrocyte markers GFAP and NCAM as described (Yang and Hernandez, 2003). Second passage cell cultures were stored in RPMI 1640 with 10% DMSO in liquid nitrogen until use.

extract_protocol: Total RNA was extracted using Qiagen RNeasy mini kits (Qiagen, Valencia, CA). RNA was then purified and quantified by measuring absorbance at 260 nm. Quality and intactness of the RNA was assessed by capillary electrophoresis analysis using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: African American, female, age 53, glaucoma


title: VREI_F034_5-18-05

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

description: Biological replicate 3 of 4. deps-1 vs wild type

hyb_protocol: Sample was incubated in hybridization buffer (4x SSC, 0.2%SDS, 0.3ug/ul poly A) at 95°C for 5 min, and samples were applied to microarrays and enclosed in submersible hybridization chambers at 65°C overnight. Slides were washed with 2x SSC/0.1% SDS, 0.2x SSC, and 0.1x SSC for 1' each and dried before scanning.

scan_protocol: Scanned on a Genepix 4000B scanner.

data_processing: normalized; background subtracted VALUE data obtained from log of processed Green signal/processed Red signal.

organism: Caenorhabditis elegans

source_name: amplified RNA from dissected gonads from wild type adults labeled with Cyanine-5 (red).

label_protocol: 5 ug of amplified RNA was primed with random hexamers at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dCTP, dGTP, with 25 µM dTTP, 25 µM Cy3-labeled dUTP (NEN Life Science, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with NaOH, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

extract_protocol: TriZol procedure

tag: dissected wild type gonad RNA from young adults

source_name: amplified RNA from dissected gonads from deps-1(bn124) adults labeled with Cyanine-3 (green).

label_protocol: 5 ug of amplified RNA was primed with random hexamers at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dCTP, dGTP, with 25 µM dTTP, 25 µM Cy5-labeled dUTP (NEN Life Science, Boston, MA), and RNase inhibitor (Invitrogen). RNA was then degraded with NaOH, and labeled cDNAs were purified using QIAquick PCR columns (Qiagen).

tag: dissected deps-1(bn124) gonad RNA from young adults


title: 05-16L-rep1

description:
05-16L a
African American with glaucoma

tag: African American, female, age 56, glaucoma


title: VREI_F035_5-17-05


title: arcAK_anaerobic_1

city: Hangzhou

first: haichun

last: gao

address: 388 Yuhangtang Rd.

country: China

institute: Zhejiang University

description: Global Transcriptome Analysis of the Cold Shock Response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold-shock proteins. J. Bacteriol. 2006 188: 4560-4569.

hyb_protocol: The two labeled cDNA pools (wild type and mutant) to be compared were mixed and hybridized simultaneously to the array on UltraGAPS slides (Corning) in a solution containing 5x SSC, 0.1% SDS, and  0.1 mg/mL of herring sperm DNA (Gibco BRL).  The entire process of hybridization, including prehybridization, hybridization, and post-hybridization wash, was performed according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned using the confocal laser microscope of the ScanArray Gx Microarray Analysis System (PerkinElmer) at a resolution of 5 µm per pixel. Scanning parameters (laser power and photomultiplier tube or PMT gain) were adjusted, so that overall intensities in both fluorescence channels were relatively equal and few spots were saturated.

data_processing: To determine fluorescence intensity (pixel density) and background intensity, 16-bit TIFF scanned images were analyzed using the software ImaGene version 7.0 (Biodiscovery). The text files from ImaGene were then analyzed with the software GeneSpring GX (Agilent).

organism: Shewanella oneidensis

source_name: ArcA

label_protocol: Fluorescently labeled cDNA copies of total cellular RNA extracted from wild-type and mutant cells were prepared by incorporation of fluorescein-labeled nucleotide analogs during a first-strand reverse transcription reaction according to the manufacturer's instructions (Invitrogen). RNA from the wild-type strain was fluorescently labeled with Cy3, and that from the mutant was labeled with Cy5.

extract_protocol: Total cellular RNAs from wild-type and arcA mutant strains of S. oneidensis were isolated using the TRIzol Reagent (Gibco BRL) according to the manufacturer's instructions. After precipitation, RNA samples were purified with the Qiagen RNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

tag: ArcA mutant grown anaerobically to exponential phase in M1 medium

source_name: wild-type MR-1

tag: MR-1 grown anaerobically to exponential phase in M1 medium


title: arcAK_aerobic_2

tag: ArcA mutant grown aerobically to exponential phase in M1 medium

tag: MR-1 grown aerobically to exponential phase in M1 medium


title: arcAK_anaerobic_3


title: 04-24R-rep2

description:
04-24R b
African American with glaucoma


title: 05-16L-rep2

description:
05-16L b
African American with glaucoma


title: arcAK_aerobic_1


title: arcAK_anaerobic_4


title: arcAK_aerobic_3


title: 04-20L-rep2

description:
04-20L b
African American with glaucoma

tag: African American, male, age 67, glaucoma


title: VREI_F033_5-18-05

data_processing: normalized; background subtracted VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: amplified RNA from dissected gonads from deps-1(bn124) adults labeled with Cyanine-5 (red).

tag: deps-1(bn124) dissected gonad RNA from young adults

source_name: amplified RNA from dissected gonads from wild type adults labeled with Cyanine-3 (green).

tag: wild type dissected gonad RNA from young adults


title: 05-14L-rep2

description:
05-14L b
African American

hyb_protocol: Purified biotin-labeled cRNA was fragmented before the hybridization. Hybridization of the labeled cRNA to Human Genome U133A and U133A 2.0 chips (Affymetrix, Santa Clara, CA) was carried out by using Genechip Instrument System (Affymetrix) at the Genechip Core Facility of Washington University (Saint Louis, MO).

data_processing: The Hu133av2 and Hu133a data were first separately normalized by using RMA method. Then the data were combined based on the common probeset Ids (Hu133a's Probeset Ids) and followed by quantile normalization to reduce the batch effects.

source_name: Human optic nerve head astrocytes, normal

tag: African American, male, age 38, normal


title: 04-20L-rep1

description:
04-20L a
African American with glaucoma


title: arcAK_aerobic_4


title: arcAK_anaerobic_2


title: VREI_F032_5-18-05

description: Biological replicate 4 of 4. deps-1 vs wild type

source_name: amplified RNA from dissected gonads from deps-1(bn124) adults labeled with Cyanine-5 (red)


title: Azaspiracid_Jurkat_24 hr_array #159_-

description: 24 hr exposure

hyb_protocol: Microarrays were imaged using an Agilent microarray scanner. Images were extracted with Agilent Feature Extraction software version A7.5.1 and data analyzed with the Rosetta Luminator 3.0 gene expression analysis system (Rosetta Informatics, Seattle, WA, USA). Using a rank consistency filter, features were subjected to a combination linear and LOWESS normalization algorithm (www.agilent.com). Based on the Rosetta error model designed for the Agilent platform, a composite array was generated at each time point, in which the data for each feature underwent a weighted averaging based on feature quality in the replicate arrays making up the composite.

scan_protocol: Arrays were scanned with an Agilent microarray scanner at a 10 um scan resolution.  Scans were with both the red and green PMT concurrently.  Adjustments were made to the PMT intensity as necessary.

treatment_protocol: For each experimental replicate (n = 2), 60 ml of cell culture were centrifuged at 1000 x g for 7 min and resuspended in 40 ml of fresh RPMI medium supplemented with FBS. Freshly resuspended cells were inoculated into 35 mm Petri dishes containing 2 ml total volume. Total cell numbers per dish ranged between 4.4 and 10.6 x 106 cells for the biological replicates at each time point. Cells were grown for >12 hr prior to addition of AZA-1 (10 nM final; 3-fold the 24 hr EC50; Twiner et al. (2005)) or equivalent amounts of methanolic vehicle (0.1% final) in order to allow recovery from any stress induced by centrifugation. The cells were harvested for RNA extractions at 1, 4, and 24 hr.

source_name: Control MeOH


title: 05-14L-rep1

description:
05-14L a
African American


title: 05-8R-rep1

description:
05-8R a
African American

tag: African American, male, age 62, normal


title: 05-13L-rep1

description:
05-13L a
African American

tag: African American, male, age 73, normal


title: Azaspiracid_Jurkat_4hr_154_+

description: 4 hr exposure

hyb_protocol: Microarrays were imaged using an Agilent microarray scanner.  Images were extracted with Agilent Feature Extraction software version A7.5.1 and data analyzed with the Rosetta Luminator 3.0 gene expression analysis system (Rosetta Informatics, Seattle, WA, USA).  Using a rank consistency filter, features were subjected to a combination linear and LOWESS normalization algorithm (www.agilent.com).  Based on the Rosetta error model designed for the Agilent platform, a composite array was generated at each time point, in which the data for each feature underwent a weighted averaging based on feature quality in the replicate arrays making up the composite.

source_name: Jurkat cells exposed to 0.1% MeOH V/V

label_protocol: Four hundred nanograms of total RNA from each time-matched control and treatment sample were amplified separately and labeled with either Cy3 or Cy5 conjugated CTP (Perkin Elmer, Boston, MA, USA) with a low input linear amplification kit (Agilent Technologies, Palo Alto, CA, USA) according to manufacturer’s protocol.  After labeling and clean up, amplified RNA was quantified by UV-vis spectroscopy.  One microgram each of Cy3- and Cy5-labeled targets were combined and hybridized to an Agilent whole human genome oligonucleotide microarray (cat.# G4112A) array for 17 hr at 60°C.  After hybridization, arrays were washed consecutively in solutions of 6X SSPE with 0.005% N-lauroylsarcosine and 0.06X SSPE with 0.005% N-lauroylsarcosine for 1 minute each at room temperature, followed by a 30 s rinse in Agilent stabilization and drying solution.  Biological replicates, including a dye swap, were performed at each time point.

growth_protocol: Human Jurkat E6-1 lymphocyte T cells (American Type Culture Collection #TIB-152; Manassas, VA, USA) were grown in RPMI medium supplemented with 10% (v/v) fetal bovine serum (FBS) and maintained in humidified 5%:95% CO2:air at 37 oC.  Cells were subcultured every 5 to 7 days with fresh medium by transferring 1 ml of cells to 9 ml of fresh supplemented medium in 75 cm^2 screw cap culture flasks.

treatment_protocol: For each experimental replicate (n = 2), 60 ml of cell culture were centrifuged at 1000 x g for 7 min and resuspended in 40 ml of fresh RPMI medium supplemented with FBS.  Freshly resuspended cells were inoculated into 35 mm Petri dishes containing 2 ml total volume.  Total cell numbers per dish ranged between 4.4 and 10.6 x 106 cells for the biological replicates at each time point.  Cells were grown for >12 hr prior to addition of AZA-1 (10 nM final; 3-fold the 24 hr EC50; Twiner et al. (2005)) or equivalent amounts of methanolic vehicle (0.1% final) in order to allow recovery from any stress induced by centrifugation.  The cells were harvested for RNA extractions at 1, 4, and 24 hr.

tag: Human Jurkat E6-1 lymphocyte T cells (ATCC# TIB-152)


title: 05-8R-rep2

description:
05-8R b
African American


title: Azaspiracid_Jurkat_1hr_ array 156_+

description: 1hr exposure

extract_protocol: Immediately following centrifugation at 1000 x g for 5 min, cells were disrupted by resuspending in 1 ml Tri-Reagent (Molecular Research Center, Inc., Cincinnati, OH, USA). All samples were processed according to manufacturer’s protocol. Total RNA was resuspended in DEPC water, purified with a Qiagen RNeasy column (Valencia, CA, USA), and quantified by UV-vis spectroscopy. The RNA was then qualified on an Agilent 2100 Bioanalyzer (Palo Alto, CA, USA) to confirm the yield of high quality RNA.


title: 04-21R-rep1

description:
04-21R a
African American

tag: African American, male, age 57, normal


title: 05-4L-rep2

description:
05-4L b
African American

tag: African American, female, age 47, normal


title: 04-15L-rep2

description:
04-15L b
African American

tag: African American, female, age 70, normal


title: UP43 CD133+ uncult vs REF

status: Public on Mar 01 2008

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: 50% formamide/GE healthcare hyb buffer, 42 degrees for 3 nights.

hyb_protocol: Corresponding control and treated samples labelled with different fluorophores were combined in a 50 ul hybridisation mix (19 ul Microarray Hybridisation Solution purchased from GE Healthcare and 50% deionised formamide) and heated at 70°C for 2 min and then at 37°C for 10 min. Sample was pipetted onto a microarray slide and covered with a glass cover slip. A 150ul aliquot of 6 X SSPE was pipetted underneath the slide to prevent dehydration. The hybridisation chamber was sealed and incubated at 42°C for 72 h. Type 7* slides were washed three times in 4 X SSPE, 10 mM EDTA pH 8.0 as above, followed by a 10 s wash in 50% deionised formamide, 6 X SSPE, before a brief rinse in HPLC grade water and drying with nitrogen gas.

scan_protocol: Scanner: Axon4000B-1. Voltage: 480,450. Resolution (micrometers): 10.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.

source_name: UP43 CD133+ uncultured(Uncultured prostate primary epithelial cells. CD133+ cells sorted from alpha2 beta1 high population using Miltenyi magnetic bead system)

label_protocol: Total RNA (4 ug) was reversed transcribed into cDNA and fluorescently labelled with Cy3 or Cy5 mono-reactive dyes (Amersham Biosciences, UK) using the Invitrogen Indirect cDNA Labelling Kit protocol (Invitrogen, UK) according to the manufacturer's instructions. After labelling, repetitive sequences within the cDNA samples were blocked with 16 ug Human Cot-1 DNA (Invitrogen, UK) to prevent non-specific sequences binding to the cDNA probes.

extract_protocol: Extraction of RNA from low cell numbers.  Column based.

tag: gender

value: male

tag: tissue type

value: normal

source_name: Human Pooled Reference RNA(BD Biosciences Human Pooled Reference RNA. )

extract_protocol: Purchased from BD Biosciences

tag: subset

value: Pooled human reference


title: 05-7L-rep2

description:
05-7L b
African American

tag: African American, male, age 70, normal


title: 05-13L-rep2

description:
05-13L b
African American


title: 03-6R-rep2

description:
03-6R c
African American

tag: African American, male, age 45, normal


title: 04-2R-rep2

description:
04-2R b
Caucasian American

tag: Caucasian American, male, age 65, normal


title: 04-21R-rep2

description:
04-21R b
African American


title: 05-11R-rep2

description:
05-11R b
Caucasian American

tag: Caucasian American, male, age 68, normal


title: 05-4L-rep1

description:
05-4L a
African American


title: 05-11R-rep1

description:
05-11R a
Caucasian American


title: 03-6R-rep1

description:
03-6R a
African American


title: 05-7L-rep1

description:
05-7L a
African American


title: 03-19L-rep2

description:
03-19L c
African American

tag: African American, male, age 56, normal


title: 04-15L-rep1

description:
04-15L a
African American


title: Azaspiracid_Jurkat_1hr_158_-

description: 1hr exposure


title: 03-19L-rep1

description:
03-19L a
African American


title: 05-5L-rep1

description:
05-5L a
Caucasian American

tag: Caucasian American, male, age 56, normal


title: Azaspiracid_Jurkat_4hr_157_-

description: 4 hr exposure


title: Azaspiracid_Jurkat_24 hr_array #155_+

description: 24 hr exposure


title: 05-5L-rep2

description:
05-5L b
Caucasian American


title: 04-4L-rep2

description:
04-4L b
Caucasian American

tag: Caucasian American, male, age 42, normal


title: 04-6L-rep1

description:
04-6L a
Caucasian American

tag: Caucasian American, male, age 57, normal


title: 04-19L-rep1

description:
04-19L a
Caucasian American

tag: Caucasian American, male, age 50, normal


title: 04-4L-rep1

description:
04-4L a
Caucasian American


title: 03-13L-rep1

description:
03-13L a
Caucasian American

tag: Caucasian American, female, age 72, normal


title: 04-2R-rep1

description:
04-2R a
Caucasian American


title: 03-11R-rep1

description:
03-11R a
Caucasian American

tag: Caucasian American, female, age 68, normal


title: 04-19L-rep2

description:
04-19L b
Caucasian American


title: 03-13L-rep2

description:
03-13L c
Caucasian American


title: 03-1L-rep2

description:
03-1Lc
Caucasian American

tag: Caucasian American, male, age 49, normal


title: 02-3L-rep3

description:
02-3Lc
African American


title: 02-3L-rep2

description:
02-3Lb
African American


title: 03-1L-rep1

description:
03-1La
Caucasian American


title: 99-9L-rep1

description:
99-9L
Caucasian American

tag: Caucasian American, female, age 46, normal


title: 04-6L-rep2

description:
04-6L b
Caucasian American


title: 02-5R-rep3

description:
02-5Rc
African American

tag: African American, male, age 43, normal


title: 00-6L-rep1

description: Caucasian American with glaucoma

tag: Caucasian American, female, age 56, glaucoma


title: 02-6L-rep1

description:
02-6La
African American

tag: African American, male, age 64, normal


title: 02-6L-rep3

description:
02-6Lc
African American


title: 02-6L-rep2

description:
02-6Lb
African American


title: 03-11R-rep2

description:
03-11R c
Caucasian American


title: 02-5R-rep2

description:
02-5Rb
African American


title: 02-3L-rep1

description:
02-3La
African American

tag: African American, female, age 70, normal


title: LC76-rep1

description:
LC76a
Caucasian American

tag: Caucasian American, female, age 76, normal


title: LC76-rep2

description:
LC76b
Caucasian American


title: LC76-rep3

description:
LC76c
Caucasian American


title: 02-5R-rep1

description:
02-5Ra
African American


title: 01-1R-rep3

description:
01-1Rc
Caucasian American

tag: Caucasian American, male, age 52, normal


title: 99-9L-rep3

description:
99-9Lc
Caucasian American


title: 99-9L-rep1

description:
99-9La
Caucasian American

tag: Caucasian American, male, age 46, normal


title: 99-9L-rep2

description:
99-9Lb
Caucasian American


title: 01-1R-rep2

description:
01-1Rb
Caucasian American


title: 01-1R-rep1

description:
01-1Ra
Caucasian American


title: NOB0308_NBE_Xba

status: Public on Jan 07 2008

type: genomic

city: Bethesda

first: Howard

last: Fine

state: MD

address: 9030 Old Georgetown Rd

department: Neurological Disorders and Stroke

institute: National Cancer Institute

description: Snap-frozen sections of areas immediately adjacent to the region used for the histopathologic diagnosis

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures using high-resolution microarray scanner 3000, GCOS 1.2

data_processing: DAT and CEL files were processed by Affymetrix GCOS 1.2 with default analysis settings. Calls generated by GDAS 3.0 with confidence threshold 0.25. Copy numbers were generated by Affymetrix Chromosome Copy Number Tool, which uses reference set of 145 normal individuals.

molecule: genomic DNA

source_name: Tumor initiating cells derived from primary glioblastoma patients at National Institutes of Health

label_protocol: Standard Affymetrix procedures

growth_protocol: TICs were established by culturing primary glioblastoma tissues in serum-free media supplemented with FGF2 and EGF.

extract_protocol: Extraction of genomic DNA with high molecular weight was performed using QIamp micro DNA extraction kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

tag: Cells

value: primary brain tumor cells, Histopathological diagnosis:glioblastoma


title: NOB1228_NBE_Xba


title: NOB0822_NBE_Xba


title: Ventricle Animal 306 zeitgeber time 21 Wildtype

status: Public on Jan 01 2008

city: Houston

first: Molly

last: Bray

state: TX

address: 1100 Bates, Suite 8070

department: Pediatrics/USDA/ARS Children's Nutrition Research Ctr

institute: Baylor College of Medicine

description: Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.

hyb_protocol: A total of 1.5 micrograms of biotin-labeled cRNA was applied to a BeadChip and allowed to hybridize overnight at 55°C for approximately 18 hours, followed by washing and staining with strepavidini-Cy3 prior to visualization.

scan_protocol: BeadChips were visualized using the BeadStation scanner, which uses a dual-laser confocal scanner with 0.8 µm resolution to determine fluorescence values for each bead on the chip.

data_processing: After scanning the probe arrays, the resulting images were analyzed using the BeadStudio software (V3, Illumina, Inc., San Diego, CA), which calculates the mean fluorescence signal across all replicates of each gene/transcript, along with a probability that the mean signal for each gene/transcript on the chip is greater than background (i.e., detection p-value).  Both non-normalized and normalized (qspline) data were generated for each tissue type.

organism: Mus musculus

source_name: Ventricles

label_protocol: Total RNA was converted to cDNA by reverse transcription using Superscript II reverse transcriptase and T7-(dT)24 primers, followed by second-strand synthesis to generate double-stranded cDNA.

extract_protocol: RNA was extracted from all tissues using a standard protocol and Tri-reagent.

treatment_protocol: Atrial and ventricular tissue samples were collected from wildtype and transgenic animals lacking a functional circadian clock within the cardiomyocytes every three hours for a period of 24 hours (n=4 samples per time point).

tag: Wildtype

tag: zeitgeber time 21


title: Ventricle Animal 270 zeitgeber time 15 Wildtype

tag: zeitgeber time 15


title: Ventricle Animal 317 zeitgeber time 12 Wildtype

tag: zeitgeber time 12


title: NOB0211_NBE_Xba


title: Ventricle Animal 234 zeitgeber time 21 Wildtype


title: Ventricle Animal 298 zeitgeber time 18 Wildtype

tag: zeitgeber time 18


title: Ventricle Animal 290 zeitgeber time 12 Wildtype


title: Ventricle Animal 271 zeitgeber time 18 Wildtype


title: Ventricle Animal 303 zeitgeber time 21 Wildtype


title: Ventricle Animal 220 zeitgeber time 12 Wildtype


title: Ventricle Animal 268 zeitgeber time 15 Wildtype


title: Ventricle Animal 321 zeitgeber time 18 Wildtype


title: Ventricle Animal 311 zeitgeber time 9 Wildtype

tag: zeitgeber time 9


title: Ventricle Animal 232 zeitgeber time 21 Wildtype


title: Ventricle Animal 352 zeitgeber time 15 Wildtype


title: Ventricle Animal 239 zeitgeber time 15 Wildtype


title: Ventricle Animal 228 zeitgeber time 18 Wildtype


title: Ventricle Animal 333 zeitgeber time 3 Wildtype

tag: zeitgeber time 3


title: Ventricle Animal 253 zeitgeber time 6 Wildtype

tag: zeitgeber time 6


title: Ventricle Animal 288 zeitgeber time 9 Wildtype


title: Ventricle Animal 285 zeitgeber time 6 Wildtype


title: Ventricle Animal 219 zeitgeber time 12 Wildtype


title: Ventricle Animal 296 zeitgeber time 15 Wildtype


title: Ventricle Animal 216 zeitgeber time 6 Wildtype


title: Ventricle Animal 258 zeitgeber time 9 Wildtype


title: Ventricle Animal 257 zeitgeber time 9 Wildtype


title: Ventricle Animal 281 zeitgeber time 3 Wildtype


title: Ventricle Animal 284 zeitgeber time 6 Wildtype


title: Ventricle Animal 280 zeitgeber time 3 Wildtype


title: Ventricle Animal 304 zeitgeber time 21 Transgenic

tag: Transgenic


title: Ventricle Animal 231 zeitgeber time 21 Transgenic


title: Ventricle Animal 204 zeitgeber time 0 Wildtype

tag: zeitgeber time 0


title: Ventricle Animal 205 zeitgeber time 0 Wildtype


title: Ventricle Animal 275 zeitgeber time 18 Transgenic


title: Ventricle Animal 233 zeitgeber time 21 Transgenic


title: Ventricle Animal 279 zeitgeber time 0 Wildtype


title: Ventricle Animal 300 zeitgeber time 18 Transgenic


title: Ventricle Animal 269 zeitgeber time 15 Transgenic


title: Ventricle Animal 351 zeitgeber time 15 Transgenic


title: Ventricle Animal 250 zeitgeber time 3 Wildtype


title: Ventricle Animal 307 zeitgeber time 0 Wildtype


title: Ventricle Animal 305 zeitgeber time 21 Transgenic


title: Ventricle Animal 291 zeitgeber time 12 Transgenic


title: Ventricle Animal 315 zeitgeber time 9 Transgenic


title: Ventricle Animal 273 zeitgeber time 18 Transgenic


title: Ventricle Animal 294 zeitgeber time 15 Transgenic


title: Ventricle Animal 238 zeitgeber time 15 Transgenic


title: Ventricle Animal 218 zeitgeber time 12 Transgenic


title: Ventricle Animal 316 zeitgeber time 12 Transgenic


title: Ventricle Animal 310 zeitgeber time 9 Transgenic


title: Ventricle Animal 293 zeitgeber time 12 Transgenic


title: Ventricle Animal 287 zeitgeber time 9 Transgenic


title: Ventricle Animal 240 zeitgeber time 15 Transgenic


title: Ventricle Animal 286 zeitgeber time 6 Transgenic


title: Ventricle Animal 289 zeitgeber time 9 Transgenic


title: Ventricle Animal 283 zeitgeber time 6 Transgenic


title: Atrium Animal 234 zeitgeber time 21 Wildtype

source_name: Atria


title: Ventricle Animal 282 zeitgeber time 3 Transgenic


title: Ventricle Animal 237 zeitgeber time 3 Transgenic


title: Ventricle Animal 215 zeitgeber time 6 Transgenic


title: Ventricle Animal 217 zeitgeber time 6 Transgenic


title: Ventricle Animal 251 zeitgeber time 3 Transgenic


title: Ventricle Animal 206 zeitgeber time 0 Transgenic


title: Ventricle Animal 235 zeitgeber time 3 Transgenic


title: Ventricle Animal 309 zeitgeber time 0 Transgenic


title: Atrium Animal 303 zeitgeber time 21 Wildtype


title: Ventricle Animal 277 zeitgeber time 0 Transgenic


title: Ventricle Animal 276 zeitgeber time 0 Transgenic


title: Atrium Animal 270 zeitgeber time 15 Wildtype


title: Atrium Animal 296 zeitgeber time 15 Wildtype


title: Atrium Animal 352 zeitgeber time 15 Wildtype


title: Atrium Animal 268 zeitgeber time 15 Wildtype


title: Atrium Animal 298 zeitgeber time 18 Wildtype


title: Atrium Animal 232 zeitgeber time 21 Wildtype


title: Atrium Animal 271 zeitgeber time 18 Wildtype


title: Atrium Animal 317 zeitgeber time 12 Wildtype


title: Atrium Animal 321 zeitgeber time 18 Wildtype


title: Atrium Animal 306 zeitgeber time 21 Wildtype


title: Atrium Animal 228 zeitgeber time 18 Wildtype


title: Atrium Animal 290 zeitgeber time 12 Wildtype


title: Atrium Animal 284 zeitgeber time 6 Wildtype


title: Atrium Animal 219 zeitgeber time 12 Wildtype


title: Atrium Animal 250 zeitgeber time 3 Wildtype


title: Atrium Animal 258 zeitgeber time 9 Wildtype


title: Atrium Animal 311 zeitgeber time 9 Wildtype


title: Atrium Animal 257 zeitgeber time 9 Wildtype


title: Atrium Animal 288 zeitgeber time 9 Wildtype


title: Atrium Animal 220 zeitgeber time 12 Wildtype


title: Atrium Animal 285 zeitgeber time 6 Wildtype


title: Atrium Animal 253 zeitgeber time 6 Wildtype


title: Atrium Animal 307 zeitgeber time 0 Wildtype


title: Atrium Animal 280 zeitgeber time 3 Wildtype


title: Atrium Animal 233 zeitgeber time 21 Transgenic


title: Atrium Animal 216 zeitgeber time 6 Wildtype


title: Atrium Animal 205 zeitgeber time 0 Wildtype


title: Atrium Animal 333 zeitgeber time 3 Wildtype


title: Atrium Animal 279 zeitgeber time 0 Wildtype


title: Atrium Animal 304 zeitgeber time 21 Transgenic


title: Atrium Animal 281 zeitgeber time 3 Wildtype


title: Ventricle Animal 252 zeitgeber time 3 Wildtype


title: Atrium Animal 305 zeitgeber time 21 Transgenic


title: Atrium Animal 273 zeitgeber time 18 Transgenic


title: Atrium Animal 204 zeitgeber time 0 Wildtype


title: Atrium Animal 231 zeitgeber time 21 Transgenic


title: Atrium Animal 240 zeitgeber time 15 Transgenic


title: Atrium Animal 300 zeitgeber time 18 Transgenic


title: Atrium Animal 269 zeitgeber time 15 Transgenic


title: Atrium Animal 351 zeitgeber time 15 Transgenic


title: Atrium Animal 293 zeitgeber time 12 Transgenic


title: Atrium Animal 294 zeitgeber time 15 Transgenic


title: Atrium Animal 310 zeitgeber time 9 Transgenic


title: Atrium Animal 275 zeitgeber time 18 Transgenic


title: Atrium Animal 289 zeitgeber time 9 Transgenic


title: Atrium Animal 218 zeitgeber time 12 Transgenic


title: Atrium Animal 238 zeitgeber time 15 Transgenic


title: Atrium Animal 316 zeitgeber time 12 Transgenic


title: Atrium Animal 291 zeitgeber time 12 Transgenic


title: Atrium Animal 315 zeitgeber time 9 Transgenic


title: Atrium Animal 215 zeitgeber time 6 Transgenic


title: Atrium Animal 287 zeitgeber time 9 Transgenic


title: Atrium Animal 217 zeitgeber time 6 Transgenic


title: Atrium Animal 283 zeitgeber time 6 Transgenic


title: Atrium Animal 286 zeitgeber time 6 Transgenic


title: Atrium Animal 282 zeitgeber time 3 Transgenic


title: Control +DOX at -DOX 50% survival, biological rep 4

city: Los Angeles

first: Diana

last: Abdueva

state: CA

address: 443 S San Pedro St, STE 403

institute: USC

description: Gene expression data from Control +DOX at -DOX 50% survival

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr to GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Gene expression measures were computed using the Robust Multichip Average (RMA) {Irizarry, 2003} in the Affy package for the R statistical programming language

organism: Drosophila melanogaster

source_name: Adult male progeny resulting from the cross between Oregon R control strain and the rtTA(3)E2 transactivator line

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

growth_protocol: cultured at 25oC in urine specimen bottles

extract_protocol: 35 mg RNA was isolated from groups of 30 adult male Drosophila using the RNAqueous kit (Ambion)

treatment_protocol: Adult control flies treated with doxycycline

tag: Line

value: control line

tag: DOX Condition

value: Plus

tag: Age

value: 50% survival of DOX- flies (~day 73)


title: Atrium Animal 309 zeitgeber time 0 Transgenic


title: Atrium Animal 251 zeitgeber time 3 Transgenic


title: Atrium Animal 235 zeitgeber time 3 Transgenic


title: Control +DOX at -DOX 50% survival, biological rep 1


title: Atrium Animal 237 zeitgeber time 3 Transgenic


title: Control +DOX at -DOX 50% survival, biological rep 3


title: Atrium Animal 206 zeitgeber time 0 Transgenic


title: Atrium Animal 276 zeitgeber time 0 Transgenic


title: Control +DOX at -DOX 50% survival, biological rep 2


title: 1B9_P2_H_EX2_POS

city: Tokyo

first: Yasuhito

last: Nannya

address: BUnkyo-ku Hongo 7-3-1

department: Department of Hematology/Oncology

country: Japan

institute: Tokyo University

description: Compared with pooled sample from CTL negative clones.

hyb_protocol: Following fragmentation, 5 microg of DNA were hybridized for 16 hr on GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: genotype-calling Dynamic Model algorithm 3.0; CNAG software.

source_name: pooled DNA for CTL-1B9 reactive clones

label_protocol: Biotinylated genomic DNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Genomic DNA were extracted using conventional methods. DNA concentrations were measured and adjusted to 50 μg/ml using the PicoGreen dsDNA Quantitation Reagent (Molecular Probes, Eugene, OR).

tag: Pooled DNA sample of 57 human B-LCLs that show positive reactivity for CTL-1B9.


title: Atrium Animal 277 zeitgeber time 0 Transgenic


title: 1B9_P2_H_EX1_NEG

description: Compared with pooled sample from CTL positive clones.

source_name: pooled DNA for CTL-1B9 non-reactive clones

tag: Pooled DNA sample of 38 human B-LCLs that show negative reactivity for CTL-1B9.


title: 1B9_P2_H_EX1_POS


title: 1B9_P1_H_EX1_NEG


title: 1B9_P1_H_EX2_NEG


title: 1B9_P2_H_EX2_NEG


title: 2A12_P1_H_EX2_POS

source_name: pooled DNA for CTL-2A12 reactive clones

tag: Pooled DNA sample of 44 human B-LCLs that show positive reactivity for CTL-2A12.


title: 1B9_P1_H_EX2_POS


title: 2A12_P1_H_EX2_NEG

source_name: pooled DNA for CTL-2A12 non-reactive clones

tag: Pooled DNA sample of 44 human B-LCLs that show negative reactivity for CTL-2A12.


title: 2A12_P1_H_EX1_NEG


title: 1B9_P1_H_EX1_POS


title: 1B9_P2_X_EX2_NEG


title: 1B9_P2_X_EX1_NEG

tag: Pooled DNA sample of 38 human B-LCLs that show negative reactivity for CTL-1B9


title: 1B9_P1_X_EX2_NEG


title: 1B9_P1_X_EX1_NEG


title: 1B9_P2_X_EX2_POS


title: 2A12_P1_H_EX1_POS


title: 1B9_P1_X_EX1_POS


title: 2A12_P1_N_EX2_POS


title: 2A12_P1_X_EX2_POS


title: 2A12_P1_X_EX2_NEG


title: 1B9_P2_N_EX1_NEG


title: 2A12_P1_X_EX1_NEG

tag: Pooled DNA sample of 44 human B-LCLs that show negative  reactivity for CTL-2A12.


title: 2A12_P1_X_EX1_POS


title: 2A12_P1_N_EX2_NEG


title: 2A12_P1_N_EX1_NEG


title: 2A12_P1_N_EX1_POS


title: 1B9_P1_N_EX2_NEG


title: Male d110 - 1

status: Public on Dec 29 2007

city: Nantes

first: Daniel

last: BARON

state: Loire-Atlantique (44)

address: 30 Bd Jean Monnet

department: UMR1064 - Centre de Recherche en Transplantation & Immunologie

country: France

institute: Institut national de la santé et de la recherche médicale-INSERM

description: Male d110 - 1 [pool 1 of male gonads sampled at d110]

hyb_protocol: A first hybridization was performed using a 33P-labelled oligonucleotide (TAATACGACTCACTATAGGG which is found at the extremity of each PCR product) to monitor the amount of cDNA present in each spot. After stripping (3 hours 68°C, 0.1 SSC, 0.2% SDS), arrays were prehybridized for 4 h at 65°C in hybridization solution (5X Denhardt's, 5 SSC, 0.5% SDS) and hybridized with denatured labeled cDNAs for 48 h at 65°C in hybridization solution.

scan_protocol: arrays were exposed to phosphor-imaging plates before scanning using a FUJI BAS 5000 at 25 µm

data_processing: Signal intensities were quantified using ArrayGauge software (Fuji Ltd, Tokyo, Japan). Low oligonucleotide signals (lower than three times the background level) were excluded from the analysis. After this filtering step, signal for each spot was divided by the hybridisation signal obtained with the vector oligonucleotide. After this correction, signals were then normalized by dividing each gene expression value by the median value of the array.

organism: Oncorhynchus mykiss

source_name: pool (1) of normal male gonads (XY) sampled 110 days (d110) after the first feeding (d0)

label_protocol: Complex target were prepared from 1 µg of RNA of each sample by simultaneous reverse transcription and labelled for 2 hours at 42°C in the presence of 30 µCi [alpha-33P] dCTP, 120 µM dCTP, 20 mM each dATP, dTTP, dGTP and 400 units Superscript II reverse transcriptase (Invitrogen). RNA was degraded by treatment at 68°C for 30 min with l µl 10% SDS, l µl 0.5M EDTA and 3 µl 3M NaOH, and then equilibrated at room temperature for l5 min. Neutralization was done by adding 10 µl 1M Tris-HCI plus 3 µl 2N HCl.

extract_protocol: Total RNA extraction: total RNA was extracted using TRIzol reagent (Invitrogen, Cergy Pontoise, France) as previously described [11316749]. The total RNA concentration was determined with an Agilent 2100 Bioanalyzer and the RNA 6000 LabChip® kit (Agilent Technologies, Stockport, UK) according to the manufacturers’ instructions.

treatment_protocol: Animals and samplings: All-male (male control group ‘Male’) and all-female (female control group ‘Female’) rainbow trout populations were obtained at the INRA experimental fish farm (Sizun, France) as previously described [10471475] Treatment with androgens (female treated Group ‘Female11ß’) was carried out as previously described [11748604]. In each group, 20 to 100 gonads, according to the age of the fish, were sampled and pooled in duplicates at various stages of development [16014816]: onset of the free swimming period after complete yolk resumption (Day 0 = D0), D0+7days (D7), occurrence of oocyte meiosis (D12), beginning of ovarian lamellar structures development (D27), occurrence of previtellogenic oocytes (D60), D90 and D110. They were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.

tag: tissue= gonads


title: 1B9_P1_N_EX2_POS


title: Male d90 - 1

description: Male d90 - 1 [pool 1 of male gonads sampled at d90]

source_name: pool (1) of normal male gonads (XY) sampled 90 days (d90) after the first feeding (d0)


title: Male d60 - 1

description: Male d60 - 1 [pool 1 of male gonads sampled at d60]

source_name: pool (1) of normal male gonads (XY) sampled 60 days (d60) after the first feeding (d0)


title: Male d27 - 2

description: Male d27 - 2 [pool 2 of male gonads sampled at d27 ; biological replicate]

source_name: pool (2) of normal male gonads (XY) sampled 27 days (d27) after the first feeding (d0)


title: Male d110 - 2

description: Male d110 - 2 [pool 2 of male gonads sampled at d110 ; biological replicate]

source_name: pool (2) of normal male gonads (XY) sampled 110 days (d110) after the first feeding (d0)


title: 1B9_P1_X_EX2_POS


title: Male d27 - 1

description: Male d27 - 1 [pool 1 of male gonads sampled at d27]

source_name: pool (1) of normal male gonads (XY) sampled 27 days (d27) after the first feeding (d0)


title: 1B9_P2_N_EX2_POS


title: 1B9_P2_N_EX1_POS


title: Male d7 - 2

description: Male d7 - 2 [pool 2 of male gonads sampled at d7 ; biological replicate]

source_name: pool (2) of normal male gonads (XY) sampled 7 days (d7) after the first feeding (d0)


title: Male d0 - 2

description: Male d0 - 2 [pool 2 of male gonads sampled at d0 ; biological replicate]

source_name: pool (2) of normal male gonads (XY) sampled at the first feeding (d0)


title: Male d0 - 1

description: Male d0 - 1 [pool 1 of male gonads sampled at d0]

source_name: pool (1) of normal male gonads (XY) sampled at the first feeding (d0)


title: Male d90 - 2

description: Male d90 - 2 [pool 2 of male gonads sampled at d90 ; biological replicate]

source_name: pool (2) of normal male gonads (XY) sampled 90 days (d90) after the first feeding (d0)


title: Male d7 - 1

description: Male d7 - 1 [pool 1 of male gonads sampled at d7]

source_name: pool (1) of normal male gonads (XY) sampled 7 days (d7) after the first feeding (d0)


title: Male d12 - 1

description: Male d12 - 1 [pool 1 of male gonads sampled at d12]

source_name: pool (1) of normal male gonads (XY) sampled 12 days (d12) after the first feeding (d0)


title: Female11b d110 - 2

description: Female11b d110 - 2 [pool 2 of female11b gonads sampled at d110 ; biological replicate]

source_name: pool (2) of female11b (androgen treatment) gonads (XX) sampled 110 days (d110) after the first feeding (d0 = beginning of the androgen treatment)


title: 1B9_P1_S_EX1_NEG


title: Female11b d110 - 1

description: Female11b d110 - 1 [pool 1 of female11b gonads sampled at d110]

source_name: pool (1) of female11b (androgen treatment) gonads (XX) sampled 110 days (d110) after the first feeding (d0 = beginning of the androgen treatment)

tag: tissue

value: gonads


title: Male d12 - 2

description: Male d12 - 2 [pool 2 of male gonads sampled at d12 ; biological replicate]

source_name: pool (2) of normal male gonads (XY) sampled 12 days (d12) after the first feeding (d0)


title: Female11b d90 - 1

description: Female11b d90 - 1 [pool 1 of female11b gonads sampled at d90]

source_name: pool (1) of female11b (androgen treatment) gonads (XX) sampled 90 days (d90 = end of the androgen treatment) after the first feeding (d0 = beginning of the androgen treatment)


title: Female11b d27 - 2

description: Female11b d27 - 2 [pool 2 of female11b gonads sampled at d27 ; biological replicate]

source_name: pool (2) of female11b (androgen treatment) gonads (XX) sampled 27 days (d27) after the first feeding (d0 = beginning of the androgen treatment)


title: Female11b d7 - 2

description: Female11b d7 - 2 [pool 2 of female11b gonads sampled at d7 ; biological replicate]

source_name: pool (2) of female11b (androgen treatment) gonads (XX) sampled 7 days (d7) after the first feeding (d0 = beginning of the androgen treatment)


title: Female11b d90 - 2

description: Female11b d90 - 2 [pool 2 of female11b gonads sampled at d90 ; biological replicate]

source_name: pool (2) of female11b (androgen treatment) gonads (XX) sampled 90 days (d90 = end of the androgen treatment) after the first feeding (d0 = beginning of the androgen treatment)


title: Female11b d12 - 2

description: Female11b d12 - 2 [pool 2 of female11b gonads sampled at d12 ; biological replicate]

source_name: pool (2) of female11b (androgen treatment) gonads (XX) sampled 12 days (d12) after the first feeding (d0 = beginning of the treatment)


title: 1B9_P1_S_EX2_POS

description: Compared with pooled sample from CTL negative clones.

source_name: pooled DNA for CTL-1B9 reactive clones


title: Female11b d12 - 1

description: Female11b d12 - 1 [pool 1 of female11b gonads sampled at d12]

source_name: pool (1) of female11b (androgen treatment) gonads (XX) sampled 12 days (d12) after the first feeding (d0 = beginning of the treatment)


title: Female11b d27 - 1

description: Female11b d27 - 1 [pool 1 of female11b gonads sampled at d27]

source_name: pool (1) of female11b (androgen treatment) gonads (XX) sampled 27 days (d27) after the first feeding (d0 = beginning of the androgen treatment)


title: 2A12_P1_S_EX1_NEG

description: Compared with pooled sample from CTL positive clones.

source_name: pooled DNA for CTL-2A12 non-reactive clones


title: Male d60 - 2

description: Male d60 - 2 [pool 2 of male gonads sampled at d60 ; biological replicate]

source_name: pool (2) of normal male gonads (XY) sampled 60 days (d60) after the first feeding (d0)


title: Female11b d60 - 2

description: Female11b d60 - 2 [pool 2 of female11b gonads sampled at d60 ; biological replicate]

source_name: pool (2) of female11b (androgen treatment) gonads (XX) sampled 60 days (d60) after the first feeding (d0 = beginning of the androgen treatment)


title: 1B9_P1_S_EX1_POS


title: 1B9_P2_S_EX1_NEG

source_name: pooled DNA for CTL-1B9 non-reactive clones


title: 1B9_P2_S_EX2_POS


title: 1B9_P2_S_EX2_NEG


title: 2A12_P1_S_EX2_NEG


title: Female11b d7 - 1

description: Female11b d7 - 1 [pool 1 of female11b gonads sampled at d7]

source_name: pool (1) of female11b (androgen treatment) gonads (XX) sampled 7 days (d7) after the first feeding (d0 = beginning of the androgen treatment)


title: Female d110 - 2

description: Female d110 - 2 [pool 2 of female gonads sampled at d110 ; biological replicate]

source_name: pool (2) of normal female gonads (XX) sampled 110 days (d110) after the first feeding (d0)


title: 1B9_P1_N_EX1_NEG


title: Female d110 - 1

description: Female d110 - 1 [pool 1 of female gonads sampled at d110]

source_name: pool (1) of normal female gonads (XX) sampled 110 days (d110) after the first feeding (d0)


title: Female d90 - 1

description: Female d90 - 1 [pool 1 of female gonads sampled at d90]

source_name: pool (1) of normal female gonads (XX) sampled 90 days (d90) after the first feeding (d0)


title: Female d90 - 2

description: Female d90 - 2 [pool 2 of female gonads sampled at d90 ; biological replicate]

source_name: pool (2) of normal female gonads (XX) sampled 90 days (d90) after the first feeding (d0)


title: Female d60 - 2

description: Female d60 - 2 [pool 2 of female gonads sampled at d60 ; biological replicate]

source_name: pool (2) of normal female gonads (XX) sampled 60 days (d60) after the first feeding (d0)


title: Female d27 - 2

description: Female d27 - 2 [pool 2 of female gonads sampled at d27 ; biological replicate]

source_name: pool (2) of normal female gonads (XX) sampled 27 days (d27) after the first feeding (d0)


title: Female d60 - 1

description: Female d60 - 1 [pool 1 of female gonads sampled at d60]

source_name: pool (1) of normal female gonads (XX) sampled 60 days (d60) after the first feeding (d0)


title: Female d27 - 1

description: Female d27 - 1 [pool 1 of female gonads sampled at d27]

source_name: pool (1) of normal female gonads (XX) sampled 27 days (d27) after the first feeding (d0)


title: Female d12 - 2

description: Female d12 - 2 [pool 2 of female gonads sampled at d12 ; biological replicate]

source_name: pool (2) of normal female gonads (XX) sampled 12 days (d12) after the first feeding (d0)


title: Female d7 - 2

description: Female d7 - 2 [pool 2 of female gonads sampled at d7 ; biological replicate]

source_name: pool (2) of normal female gonads (XX) sampled 7 days (d7) after the first feeding (d0)


title: Female d0 - 2

description: Female d0 - 2 [pool 2 of female gonads sampled at d0 ; biological replicate]

source_name: pool (2) of normal female gonads (XX) sampled at the first feeding (d0)

tag: Tissue


title: 1B9_P1_S_EX2_NEG


title: 1B9_P2_X_EX1_POS

description: Compared with pooled sample from CTL negative clones.

source_name: pooled DNA for CTL-1B9 reactive clones


title: yw ZT19c1

type: other

first: maocheng

last: yang

address: 10 Center Drive

department: NCI

institute: National Institutes of Health

description: Circadian regulation of miRNA using microarray

hyb_protocol: Loyal A. Goff, Maocheng Yang, Roberts C. Getts, Richard W. Padgett, Ronald P. Hart. (2005) Rational probe optimization and enhanced detection strategy for microRNAs using microarrays. RNA Biology 2(3): 93-100.

scan_protocol: Axon 4000B scanner

data_processing: Data filtered and normalized using Genetraffic

molecule: other

source_name: yw fly head 19 hours

extract_protocol: low molecular weight RNA by mirVANA miRNA isolation kit

tag: yw fly head 19 hours

source_name: pooled control

label_protocol: as channel 1

tag: pooled control


title: Female d7 - 1

description: Female d7 - 1 [pool 1 of female gonads sampled at d7]

source_name: pool (1) of normal female gonads (XX) sampled 7 days (d7) after the first feeding (d0)


title: yw ZT19c

label_protocol: Loyal A. Goff, Maocheng Yang, Roberts C. Getts, Richard W. Padgett, Ronald P. Hart. (2005) Rational probe optimization and enhanced detection strategy for microRNAs using microarrays. RNA Biology 2(3): 93-100.


title: 1B9_P2_S_EX1_POS


title: Female d0 - 1

description: Female d0 - 1 [pool 1 of female gonads sampled at d0]

source_name: pool (1) of normal female gonads (XX) sampled at the first feeding (d0)


title: yw ZT19b1


title: yw ZT19b


title: Female d12 - 1

description: Female d12 - 1 [pool 1 of female gonads sampled at d12]

source_name: pool (1) of normal female gonads (XX) sampled 12 days (d12) after the first feeding (d0)


title: yw ZT13c1

source_name: yw fly head 13 hours

tag: yw fly head 13 hours


title: yw ZT19a


title: 2A12_P1_S_EX2_POS

source_name: pooled DNA for CTL-2A12 reactive clones


title: 2A12_P1_S_EX1_POS


title: yw ZT13c


title: yw ZT13a


title: yw ZT19a1


title: yw ZT13b1


title: yw ZT7c

source_name: yw fly head 7 hours

tag: yw fly head 7 hours


title: yw ZT7c1


title: yw ZT13a1


title: yw ZT7b


title: yw ZT7b1


title: yw ZT13b


title: yw ZT7a1


title: yw ZT1c

source_name: yw fly head 1 hour

tag: yw fly head 1 hour


title: yw ZT1c1


title: yw ZT1b


title: cyc ZT19c1

source_name: cyc fly head 19 hours

tag: cyc fly head 19 hours


title: yw ZT1b1


title: cyc ZT19a


title: cyc ZT19b


title: cyc ZT19b1


title: cyc ZT19a1


title: Female11b d60 - 1

description: Female11b d60 - 1 [pool 1 of female11b gonads sampled at d60]

source_name: pool (1) of female11b (androgen treatment) gonads (XX) sampled 60 days (d60) after the first feeding (d0 = beginning of the androgen treatment)


title: yw ZT1a1


title: yw ZT1a


title: yw ZT7a


title: cyc ZT19c


title: cyc ZT13c

source_name: cyc fly head 13 hours

tag: cyc fly head 13 hours


title: cyc ZT13b1


title: cyc ZT13a


title: cyc ZT7c1

source_name: cyc fly head 7 hour

tag: cyc fly head 7 hour


title: cyc ZT7c


title: cyc ZT13a1


title: cyc ZT7b


title: cyc ZT13c1


title: cyc ZT13b


title: cyc ZT7b1


title: cyc ZT1c

source_name: cyc fly head 1 hour

tag: cyc fly head 1 hour


title: cyc ZT1c1

tag: pooled control same for every sample(fly head)


title: cyc ZT7a


title: cyc ZT7a1


title: cyc ZT1b


title: cyc ZT1a


title: 1B9_P2_N_EX2_NEG

description: Compared with pooled sample from CTL positive clones.

source_name: pooled DNA for CTL-1B9 non-reactive clones

tag: Pooled DNA sample of 38 human B-LCLs that show negative reactivity for CTL-1B9.


title: cyc ZT1b1


title: cyc ZT1a1

tag: cyc01 adult fly heads 1 hour

tag: universal control for every chip


title: HOXA13 ChIP (HG18 Array 1 of 2)

status: Public on Dec 28 2007

city: Stanford

first: John

middle: Louis

last: Rinn

address: 2155 CCSR 269 Campus Dr

department: Dermatology

institute: Stanford University

description: HG18 Array 1 of 2

hyb_protocol: Standard Nimblegen hybridization kits and protocols were used

scan_protocol: Arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols

data_processing: Arrays were processed using Nimblegens standard protocol for Nimblescan 2.4 ChIP data extraction

source_name: HOXA13 ChIP

label_protocol: Standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension

growth_protocol: Foreskin firbroblasts were grown in DMEM with 10% Fetal Bovine Serum until confluent and growth arrested in G0 by serum starvation for 48 hours

extract_protocol: ChIP was performed on 4x10^6 fibroblast cells and Farnham ChIP protocol was used to derive ChIP DNA and was amplified by sigma WGA2 kit for 1 round of amplification

treatment_protocol: NO additional treatments were performed

tag: primary human foreskin firbroblasts

source_name: Mock ChIP of Rabbit IGG

tag: Human primary foreskin fibroblasts


title: Stage1_Vs_Stage6_13109309

city: Urbana

first: Lila

middle: O.

last: Vodkin

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

description: Biological replicate 2   Technical replicate 1. The quantitated GPR files were then transferred to GeneSpring 7.2 Agilent Technologies (Palo Alto,CA) for further analysis. For microarray data analysis using GeneSpring 7.2, Agilent Technologies (Palo Alto, CA) we uploaded initially a soybean Genome or Array file containing the corresponding information for each one of the Oligos represented in the array. A systematic name was defined and listed along with its corresponding EST accession number, Clone ID, Blast X (cutoff 10E-06), top hit GI number and its description, top hit Arabidopsis ID and its description, corresponding gene ontologies to top hits, and associated EST’s numbers. This file was uploaded in GeneSpring 7.2 (Silicon Genetics, CA) and was used as the soybean oligo genome information for further analysis.

hyb_protocol: A total of 20 µg of the reference Stage 1 (imbibed seed) RNA was used to be labeled by reverse transcription with Cy3-dUTP and compared to 20 µg of RNA from each of stages 2-7 labeled by reverse transcription with Cy5-dUTP following the protocol by Hedge et al., 2000.  The Soybean Oligo array slides were pre-hybridized, hybridized and washed as described by Vodkin et al., 2004.  Duplicate dye swaps were set up as well.

scan_protocol: The hybridized slides were scanned with a ScanArray Express Microarray Scanner, Packard Bioscience/ PerkinElmer (Shelton, CT) and the fluorescence was quantified by using the ScanArray Gx/ProScanArray, Microarray Analysis System (Packard biosciences/Perkin Elmer, Shelton, CT) using a protocol defined by a corresponding GAL file previously generated.

data_processing: Data from a total of 48 slides, containing the intensity values for the reference and the signal channels as well as the flag values for present, absent or marginal spots was uploaded and sample attributes were defined. The data was initially transformed for dye swap for the appropriate slide samples and all the intensity values less than 0.01 or negative were converted to 0.01 to reset biologically irrelevant or otherwise unacceptable expression values. Time was defined as the only parameter to be taken into account for analysis and 6 different conditions were defined: one for each time point defined. After background subtraction and eliminating all the spots flagged as marginal or absent, data was normalized using an intensity-dependent LOWESS (locally weighted scatter plot smoothing) normalization method (Yang et al., 2002) to minimize systematic non-biological differences and standardize chips for cross-array comparisons. Normalized data was then filtered on expression level to obtain a list of genes with expression values in at least one of the comparisons made. This list was then used for statistical analysis. A Welch ANOVA (parametric test, variances not assumed equal) was carried out with a P-value cutoff 0.05, a false discovery rate (FDR) of 0.05 and between 0.1 and 100 fold expression value change. This list was further filtered on expression level creating restrictions to define relevant genes at any particular time point as well as to find expression profiles of biological relevance for the study.

organism: Glycine max

source_name: Total RNA from Soybean Cotyledons in Stage 1 of germination

label_protocol: Direct incorporation using Cy3-dUTP

growth_protocol: Four Glycine max Williams dry seeds were planted per small pot (4 inches) containing pre-wetted Universal Mix SB300 soil in the green house.

extract_protocol: McCarty D. 1986.  Phenol Chloroform, Lithium Chloride extraction                      method

tag: Cultivar Williams. Pooled cotyledons from 10 seedlings in Stage 1 of germination/4 different RNA purifications pooled

source_name: Total RNA from Soybean Cotyledons in Stage 6 of germination

label_protocol: Direct incorporation using Cy5-dUTP

tag: Cultivar Williams. Pooled cotyledons from 10 seedlings in Stage 6 of germination/4 different RNA purifications pooled


title: Stage6_Vs_Stage1_13109312

description: Biological replicate 2   Technical replicate 2. The quantitated GPR files were then transferred to GeneSpring 7.2 Agilent Technologies (Palo Alto,CA) for further analysis. For microarray data analysis using GeneSpring 7.2, Agilent Technologies (Palo Alto, CA) we uploaded initially a soybean Genome or Array file containing the corresponding information for each one of the Oligos represented in the array. A systematic name was defined and listed along with its corresponding EST accession number, Clone ID, Blast X (cutoff 10E-06), top hit GI number and its description, top hit Arabidopsis ID and its description, corresponding gene ontologies to top hits, and associated EST’s numbers. This file was uploaded in GeneSpring 7.2 (Silicon Genetics, CA) and was used as the soybean oligo genome information for further analysis.


title: Stage1_Vs_Stage5_13111942

source_name: Total RNA from Soybean Cotyledons in Stage 5 of germination

tag: Cultivar Williams. Pooled cotyledons from 10 seedlings in Stage 5 of germination/4 different RNA purifications pooled


title: Stage4_Vs_Stage1_13112078

source_name: Total RNA from Soybean Cotyledons in Stage 4 of germination

tag: Cultivar Williams. Pooled cotyledons from 10 seedlings in Stage 4 of germination/4 different RNA purifications pooled


title: 1B9_P1_N_EX1_POS

source_name: pooled DNA for CTL-1B9 reactive clones

tag: Pooled DNA sample of 57 human B-LCLs that show positive reactivity for CTL-1B9.


title: Stage3_Vs_Stage1_13048559

source_name: Total RNA from Soybean Cotyledons in Stage 3 of germination

tag: Cultivar Williams. Pooled cotyledons from 10 seedlings in Stage 3 of germination/4 different RNA purifications pooled


title: Stage1_Vs_Stage5_13111941


title: Stage1_Vs_Stage4_13112076


title: Stage6_Vs_Stage1_13109313


title: Stage1_Vs_Stage4_13108818


title: Stage1_Vs_Stage3_13048633


title: Stage4_Vs_Stage1_13112077


title: Stage2_Vs_Stage1_13108804

source_name: Total RNA from Soybean Cotyledons in Stage 2 of germination

tag: Cultivar Williams. Pooled cotyledons from 10 seedlings in Stage 2 of germination/4 different RNA purifications pooled


title: Stage2_Vs_Stage1_13108805


title: Stage1_Vs_Stage2_13112089

description: Biological replicate 2  Technical replicate 1. The quantitated GPR files were then transferred to GeneSpring 7.2 Agilent Technologies (Palo Alto,CA) for further analysis. For microarray data analysis using GeneSpring 7.2, Agilent Technologies (Palo Alto, CA) we uploaded initially a soybean Genome or Array file containing the corresponding information for each one of the Oligos represented in the array. A systematic name was defined and listed along with its corresponding EST accession number, Clone ID, Blast X (cutoff 10E-06), top hit GI number and its description, top hit Arabidopsis ID and its description, corresponding gene ontologies to top hits, and associated EST’s numbers. This file was uploaded in GeneSpring 7.2 (Silicon Genetics, CA) and was used as the soybean oligo genome information for further analysis.


title: Stage5_Vs_Stage1_13109308


title: Stage5_Vs_Stage1_13109305


title: Stage3_Vs_Stage1_13048558


title: Stage1_Vs_Stage2_13108824


title: Stage1_Vs_Stage7_13109216

description: Biological replicate 1  Technical replicate 1. The quantitated GPR files were then transferred to GeneSpring 7.2 Agilent Technologies (Palo Alto,CA) for further analysis. For microarray data analysis using GeneSpring 7.2, Agilent Technologies (Palo Alto, CA) we uploaded initially a soybean Genome or Array file containing the corresponding information for each one of the Oligos represented in the array. A systematic name was defined and listed along with its corresponding EST accession number, Clone ID, Blast X (cutoff 10E-06), top hit GI number and its description, top hit Arabidopsis ID and its description, corresponding gene ontologies to top hits, and associated EST’s numbers. This file was uploaded in GeneSpring 7.2 (Silicon Genetics, CA) and was used as the soybean oligo genome information for further analysis.

source_name: Total RNA from Soybean Cotyledons in Stage 7 of germination

tag: Cultivar Williams. Pooled cotyledons from 10 seedlings in Stage 7 of germination/4 different RNA purifications pooled


title: Stage1_Vs_Stage3_13048612


title: Stage1_Vs_Stage7_13109217

description: Biological replicate 1  Technical replicate 2. The quantitated GPR files were then transferred to GeneSpring 7.2 Agilent Technologies (Palo Alto,CA) for further analysis. For microarray data analysis using GeneSpring 7.2, Agilent Technologies (Palo Alto, CA) we uploaded initially a soybean Genome or Array file containing the corresponding information for each one of the Oligos represented in the array. A systematic name was defined and listed along with its corresponding EST accession number, Clone ID, Blast X (cutoff 10E-06), top hit GI number and its description, top hit Arabidopsis ID and its description, corresponding gene ontologies to top hits, and associated EST’s numbers. This file was uploaded in GeneSpring 7.2 (Silicon Genetics, CA) and was used as the soybean oligo genome information for further analysis.


title: Stage1_Vs_Stage6_13111935


title: Stage1_Vs_Stage7_13109219


title: Stage1_Vs_Stage6_13048613


title: Stage1_Vs_Stage7_13109218


title: Stage5_Vs_Stage1_13112056


title: Stage4_Vs_Stage1_13111966


title: Stage6_Vs_Stage1_13112062


title: Stage6_Vs_Stage1_13112080


title: Stage5_Vs_Stage1_13111947


title: Stage3_Vs_Stage1_13111946


title: Stage1_Vs_Stage5_13111944


title: Stage1_Vs_Stage6_13112058


title: Stage4_Vs_Stage1_13111965


title: Stage1_Vs_Stage4_13111969


title: Stage7_Vs_Stage1_13111943


title: Stage1_Vs_Stage4_13111959


title: Stage1_Vs_Stage2_13111949


title: Stage1_Vs_Stage5_13111951


title: Stage1_Vs_Stage3_13111950


title: Stage3_Vs_Stage1_13112088


title: Stage1_Vs_Stage2_13111952


title: Stage2_Vs_Stage1_13108803


title: Spores_germination following 2 hours of pre-incubation in nitrogen_2 hours and 30 minutes

status: Public on Dec 23 2007

city: Rehovot

first: Naama

last: Barkai

address: P.O box 26

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute of Science

description: S. cerevisiae spores pre-incubated in glucose, 2 hours and 30 minutes after the transfer to YPD

hyb_protocol: For each hybridization, labeled Cy3 and Cy5 were combined together with the following blockers: 5µg Herring sperm (Promega), 5 µg tRNA (Gibco) and 17.5µg Poly A (Synthesized oligos with the length of 40, 50 and 60), and concentrated to 25µl using Microcon (Millipore). 25 µl of hybridization x2 solution (10x SSC, 50% formamide and 0.2% SDS) was added. Microarrays containing all yeast ORFs (purchased from the Microarray Centre, University Health Network, Ontario) were pre-hybridized by incubating in a solution containing 1% BSA, 25% formamide, 5x SSC and 0.1% SDS at 42 C for 45 minutes. The slides were washed with DDW and dried by centrifugation (3 minutes, 2000 rpm). The labeled sample with the blockers, was boiled for 5 minutes, centrifuged for 1 minute and hybridized on the slide. The slides were placed in hybridization chamber (Corning) and incubated over night at 42 C. The slides were washed for 5 minutes at 42 C with a solution containing 2x SSC and 0.1% SDS. Additional wash was performed at room temperature with a solution containing 0.1x SSC and 0.1% SDS, followed by 3 additional washes at room temperature in 0.1x SSC solution.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using Aginlet's DNA microarray scanner and image intensity data were extracted and analyzed with SpotReader (Niles Scientific) analysis software.

data_processing: Background intensity was subtracted using a Bayesian correction, and the ratios of the two dyes were log2-transformed. Log2 ratios were then corrected for intensity-dependant and spatial-dependant biases by subtracting a Lowess curve followed by a median filter. The two spots corresponding to each gene were then averaged, and genes for which the two spots were significantly different were declared as 'missing values' (along with other genes which were flagged by the image analysis software or removed by manual inspection).

organism: Saccharomyces cerevisiae

label_protocol: Samples and reference cDNA were synthesized from total RNA and labeled with Cy3 and Cy5 by the indirect amino-allyl method as described below. Total RNA (20 µg) was annealed with 4 µg oligo dT12-18 and reverse transcribed into cDNA with M-MLV Reverse Transcriptase RNase H Minus (Promega) for 2 hours at 45°C in the presence of 2.5mM MgCl2, 0.5 mM of dATP, dCTP and dGTP, 0.1mM dTTP, 0.4mM amino-allyl dUTP. Additional 400U M-MLV Reverse Transcriptase RNase H Minus was added and incubated for another 2 hours. The reaction was terminated by incubation at 70°C for 15 minutes and RNA was degraded by adding 10 µM 1N NaOH and incubation at 65 C for 30 minutes. The sample was neutralized by titrating with 1M HCl. cDNA was purified by ethanol precipitation, resuspended in 10 µl 0.1M Sodium Carbonate buffer pH 9.3. Cy5 or Cy3 were added to experimental or reference sample, respectively, and incubated at 25 C for 1 hour. Labeled cDNA was purified by Strataprep PCR purification kit (Stratagene) according to the manufactures instructions. Dye incorporation was measured using a spectrophotometer.

extract_protocol: Cells were flash frozen in liquid Nitrogen. Total RNA was extracted using RNeasy Midi kit (QIAGEN)

tag: Strain

value: SK1 wild type

source_name: S. cerevisiae, logarithmic growing, haploid cells

value: SK1 wild type haploid cells, Mating types and growth conditions:Mata and Matα cells were grown separately in YPD.


title: Spores_germination following 2 hours of pre-incubation in nitrogen_3 hours and 30 minutes

description: S. cerevisiae spores pre-incubated in glucose, 3 hours and 30 minutes after the transfer to YPD


title: Spores_germination following 2 hours of pre-incubation in nitrogen_4 hours

description: S. cerevisiae spores pre-incubated in glucose, 4 hours after the transfer to YPD


title: Stage1_Vs_Stage3_13112090


title: Stage1_Vs_Stage7_13009211

description: Biological replicate 2  Technical replicate 1. The quantitated GPR files were then transferred to GeneSpring 7.2 Agilent Technologies (Palo Alto,CA) for further analysis.  For microarray data analysis using GeneSpring 7.2, Agilent Technologies (Palo Alto, CA) we uploaded initially a soybean Genome or Array file containing the corresponding information for each one of the Oligos represented in the array.  A systematic name was defined and listed along with its corresponding EST accession number, Clone ID, Blast X (cutoff 10E-06), top hit GI number and its description, top hit Arabidopsis ID and its description, corresponding gene ontologies to top hits, and associated EST’s numbers.  This file was uploaded in GeneSpring 7.2 (Silicon Genetics, CA) and was used as the soybean oligo genome information for further analysis.

data_processing: Data from a total of 48 slides, containing the intensity values for the reference and the signal channels as well as the flag values for present, absent or marginal spots was uploaded and sample attributes were defined.  The data was initially transformed for dye swap for the appropriate slide samples and all the intensity values less than 0.01 or negative were converted to 0.01 to reset biologically irrelevant or otherwise unacceptable expression values.  Time was defined as the only parameter to be taken into account for analysis and 6 different conditions were defined: one for each time point defined.  After background subtraction and eliminating all the spots flagged as marginal or absent, data was normalized using an intensity-dependent LOWESS (locally weighted scatter plot smoothing) normalization method (Yang et al., 2002) to minimize systematic non-biological differences and standardize chips for cross-array comparisons.  Normalized data was then filtered on expression level to obtain a list of genes with expression values in at least one of the comparisons made.  This list was then used for statistical analysis.  A Welch ANOVA (parametric test, variances not assumed equal) was carried out with a P-value cutoff 0.05, a false discovery rate (FDR) of 0.05 and between 0.1 and 100 fold expression value change. This list was further filtered on expression level creating restrictions to define relevant genes at any particular time point as well as to find expression profiles of biological relevance for the study.

growth_protocol: Four Glycine max Williams 43 dry seeds were planted per small pot (4 inches) containing pre-wetted Universal Mix SB300 soil in the green house.

tag: Cultivar Williams 43.  Pooled cotyledons from 10 seedlings in Stage 1 of germination.  4 different RNA preps pooled.

tag: Cultivar Williams 43.  Pooled cotyledons from 10 seedlings in Stage 7 of germination.  4 different RNA preps pooled.


title: Stage1_Vs_Stage7_13009212

description: Biological replicate 2  Technical replicate 2. The quantitated GPR files were then transferred to GeneSpring 7.2 Agilent Technologies (Palo Alto,CA) for further analysis. For microarray data analysis using GeneSpring 7.2, Agilent Technologies (Palo Alto, CA) we uploaded initially a soybean Genome or Array file containing the corresponding information for each one of the Oligos represented in the array. A systematic name was defined and listed along with its corresponding EST accession number, Clone ID, Blast X (cutoff 10E-06), top hit GI number and its description, top hit Arabidopsis ID and its description, corresponding gene ontologies to top hits, and associated EST’s numbers. This file was uploaded in GeneSpring 7.2 (Silicon Genetics, CA) and was used as the soybean oligo genome information for further analysis.


title: Stage7_Vs_Stage1_13048635


title: Stage2_Vs_Stage1_13111948


title: Spores_germination following 2 hours of pre-incubation in nitrogen_1 hour

description: S. cerevisiae spores pre-incubated in glucose, 1 hour after the transfer to YPD


title: Spores_germination following 2 hours of pre-incubation in nitrogen_30 minutes

description: S. cerevisiae spores pre-incubated in glucose, 30 minutes after the transfer to YPD


title: cadmium-fed fish

status: Public on Dec 26 2007

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

institute: Israel Oceanographic and Limnological Research

description:
All 12 hybridized slides participate in each binary comparison between exposed and the reference fish. For two Samples 1 (cadium-fed) and 2 (cadium-injected), see detailed explanations in SERIES - overall design and PROTOCOLS - data processing.
Liver, reference fish 1 (Channel 1 source) vs. cadmium-fed fish 1 (Channel 2 source) (GSM197742_325.gpr raw data file attached to Series)
Liver, cadmium-fed fish 1 (Channel 1 source) vs. cadmium-injected fish 1 (Channel 2 source) (GSM197742_338.gpr raw data file attached to Series)
Liver, cadmium-injected fish 1 (Channel 1 source) vs. reference fish 1 (Channel 2 source) (GSM197742_342.gpr raw data file attached to Series)
Liver, cadmium-fed fish 4 (Channel 1 source) vs. reference fish 4 (Channel 2 source) (GSM197742_443.gpr raw data file attached to Series)
Liver, reference fish 4 (Channel 1 source) vs. cadmium-injected fish 4 (Channel 2 source) (GSM197742_456.gpr raw data file attached to Series)
Liver, cadmium-injected fish 4 (Channel 1 source) vs. cadmium-fed fish 4 (Channel 2 source) (GSM197742_459.gpr raw data file attached to Series)
Liver, reference fish 2 (Channel 1 source) vs. cadmium-fed fish 2 (Channel 2 source) (GSM197742_451.gpr raw data file attached to Series)
Liver, cadmium-fed fish 2 (Channel 1 source) vs. cadmium-injected fish 2 (Channel 2 source) (GSM197742_858.gpr raw data file attached to Series)
Liver, cadmium-injected fish 2 (Channel 1 source) vs. reference fish 2 (Channel 2 source) (GSM197742_458.gpr raw data file attached to Series)
Liver, reference fish 3 (Channel 1 source) vs. cadmium-injected fish 3 (Channel 2 source) (GSM197742_479.gpr raw data file attached to Series)
Liver, cadmium-fed fish 3 (Channel 1 source) vs. reference fish 3 (Channel 2 source) (GSM197742_481.gpr raw data file attached to Series)
Liver, cadmium-injected fish 3 (Channel 1 source) vs. cadmium-fed fish 3 (Channel 2 source) (GSM197742_441.gpr raw data file attached to Series)

hyb_protocol: Microarray slides were incubated with pre-hybridization solution (1% BSA; 5x SSC; 0.1% SDS, 25% formamide) for 2h at 42°C to block non-specific DNA interactions, reducing background fluorescence, followed by two short rinses in water, one in ethanol and drying by mild centrifugation of vertical slides. Dual-labeled solutions, aimed at binary comparisons between two experimental conditions, were prepared by mixing the two compared labeled cDNA populations, followed by 1:1 dilution with hybridization solution containing 200 µg/ml salmon sperm DNA, 10x SSC, 0.2% SDS, 50% formamide. The heat denatured hybridization mixture (3' at 95°C) was layered onto the microarray, covered (Lifterslip, Erie Scientific; #25x60-2-4789) and incubated over night at 42°C in humidified hybridization chamber (Corning). Following incubation, slides were washed as follows: 5’ at 42°C in x2 SSC - 0.1% SDS, mild shaking for 10’ at room temperature in x0.1 SSC - 0.1% SDS; mild shaking 4x for 5’ at room temperature in x0.1 SSC, ending by two quick dips, one in water and one in ethanol. The slides were dried by centrifugation.

scan_protocol: The slides were scanned by Axon 4000B laser scanner in two wavelengths, corresponding to the Cy3 and Cy5 emissions. The TIF imaged dual fluorescence was quantified by the GENEPIX software (Molecular Devices, U.S.A.), which provided also weight index of the quality for each hybridized spot.

data_processing:
Data analysis was conducted under the R/BioConductor environment (Gentleman et al., 2005). Calculation and statistical analysis of log2 expression ratios of each unique spot across binary comparisons between each of the cadmium exposed groups and reference RNAs was carried out using the LIMMA package (Linear Models for Microarray data Analysis; Smyth, 2004, 2005). GENEPIX quantified image files were imported into LIMMA, spots with quality flags < -49 were marked as unreliable, and the Cy5 and Cy3 intensities within each slide were normalized using the print-tip Loess method. No background correction was applied. LIMMA calculated for each spot on an individual slide an M-value [M=log2(Cy5)/Cy3); Cy5 / Cy3 are the normalized emission intensities of the spot] and an emission intensity A-value [A=(log2(Cy5)*Cy3))/2]. Subsequently, LIMMA fitted a linear model to the expression data followed by Empirical Bayes smoothing. Inter-duplicate correlation method was used at the linear modeling step. A meanA value, which is the average spot emission intensity across the analyzed experiment, was calculated for each unique spot and only spots with meanA > 8.5 were included in the analysis, avoiding faint emissions. The LIMMA summary statistics of each unique spot included an estimated average M-value across each binary comparison associated to two statistical parameters: B statistic, the log-odds that the spot is differentially expressed and p-value, derived from a moderated t-statistic after multiple testing correction according to Benjamini and Hochberg (1995).     References:  Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soc Ser B 57: 289-300.  Gentleman, R., Carey, V.J., Huber, W., Irizarry, R.A., Dudoit, S. (Eds.). (2005) Bioinformatics And Computational Biology Solutions Using R and Bioconductor. Statistics for Biology and Health. Springer, 473 pp.  Smyth, G.K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3. http//www.bepress.com/sagmb/vol3/iss1/art3  Smyth, G.K. 2005. LIMMA: linear models for microarray data. In: Gentleman, R., Carey, V.J., Huber, W., Irizarry, R.A. and Dudoit, S. (Eds.) Bioinformatics and computational biology solutions using R and Bioconductor. Statistics for Biology and Health. Springer. Chapter 23: 397-420.

VALUES = Four values for each unique spot in each sample. Two descriptive parameters: M=log2(expression ratio) for each unique spot across each binary comparison of exposed vs. reference group of fish, and meanA=mean(log2(Cy5*Cy3))/2 across the entire experiment. Emissions were Lowess-normalized without background correction. Two statistical indices: P-value and B statistics.

molecule: polyA RNA

organism: Lithognathus mormyrus

source_name: Samples consists of all 12 hybridized slides with 3 cdnas, dual hybridized in all possible combinations: reference, cadium-fed, cadium-injected fish (see description for individual channel combinations)

label_protocol: Messenger RNA was labeled by the fluorescent dyes Cy3 and Cy5, using the amino allyl indirect cDNA labeling method, as follows: 200-400 ng mRNA of the transcript population was incubated for 10’ at 70°C with 100 µg dT primer (T15VN) and was immediately chilled on ice. The resulting RNA-dT primer hybrid was reverse transcribed in a total volume of 30 µl for 1h at 42°C, in a solution containing: reverse transcriptase (ImProm II, Promega #A3802; 1.5 µl/reaction), 32 units of RNase inhibitor, 3.5 mM of MgCl2 solution and 0.5 mM dNTP mix in which the dTTP was replaced by Amino Allyl-dUTP / dTTP mixture (4:1). The reverse transcription was followed by mRNA hydrolysis for 15’ at 65°C in alkaline pH (0.2 M NaOH (fresh), and 0.1 M of EDTA). The alkaline solution was neutralized by 0.35 M HEPES (pH 7.0) followed by buffer replacement and cDNA concentration, accomplished by wash x3 of the solution by 450 µl of water through Microcon YM-30 filter (Amicon, #42410) ending with a volume of 50-100 µl. The cDNAs were coupled to an aliquot of the fluorescent dyes Cy3 or Cy5 mono-reactive succinimidyl ester-derivetized NHS-ester through the reactive Amino Allyl groups. Raw dye solution was prepared from a tube of dry dye (Amersham PA23001 / PA25001 for Cy3 and Cy5, respectively) dissolved in 72 µl DMSO, divided into 8 single labeling aliquots. The reaction was carried out for 1h at room temperature in 9 µl of 0.1M fresh Na-Bicarbonate Buffer pH 9.0. Hydroxylamine was added to the solution at a final concentration of 1.33M and was incubated for 15’ at room temperature. Finally the solution was neutralized by sodium acetate, pH=5.2 to a final concentration of 72 mM and purified by affinity column-based kit (Qiaquick, Qiagen). Labeling level was evaluated by spectrophotometry at both 260 nm for cDNA estimation and 550 nm (Cy3) and 650 nm (Cy5) for labeling intensity measurement.

growth_protocol: The fish were kept before and during experimental manipulations in 700 liter clean seawater flow-through tanks under ambient temperature regime ranged 16-21°C.

extract_protocol: EZ-RNA II Kit (Biological Industries, Israel) was used for total RNA extraction. PolyTtract kit (Promega) was used for mRNA extraction from total RNA solutions.

treatment_protocol: Two groups of four fish were exposed to fed and injected CdCl2, respectively. Additional eight untreated fish were used as a reference group. Cadmium content of the food was 57.25 µg/g food and 31 food portions, each of 1% body weight were given to the fish four times a week. Fish were sacrificed three days after last feeding, receiving during the 57 days of the experiment 17.75 mg Cd/kg body weight. A dose of 2.5 mg Cd/kg body weight was intra-peritoneally injected to the other group and fish were sacrificed eight days after injection. The reference fish were fed by commercial food pellets not containing cadmium.

tag: No reproductive activity

source_name: Samples consists of all 12 hybridized slides with 3 cdnas, dual hybridized in all possible combinations: cadium-fed, cadium-injected and reference fish (see description for individual channel combinations)


title: cadmium-injected fish

description:
All 12 hybridized slides participate in each binary comparison between exposed and the reference fish. For two Samples 1 (cadium-fed) and 2 (cadium-injected), see detailed explanations in SERIES - overall design and PROTOCOLS - data processing.
Liver, reference fish 1 (Channel 1 source) vs. cadmium-fed fish 1 (Channel 2 source) (GSM197743_325.gpr raw data file attached to Series)
Liver, cadmium-fed fish 1 (Channel 1 source) vs. cadmium-injected fish 1 (Channel 2 source) (GSM197743_338.gpr raw data file attached to Series)
Liver, cadmium-injected fish 1 (Channel 1 source) vs. reference fish 1 (Channel 2 source) (GSM197743_342.gpr raw data file attached to Series)
Liver, cadmium-fed fish 4 (Channel 1 source) vs. reference fish 4 (Channel 2 source) (GSM197743_443.gpr raw data file attached to Series)
Liver, reference fish 4 (Channel 1 source) vs. cadmium-injected fish 4 (Channel 2 source) (GSM197743_456.gpr raw data file attached to Series)
Liver, cadmium-injected fish 4 (Channel 1 source) vs. cadmium-fed fish 4 (Channel 2 source) (GSM197743_459.gpr raw data file attached to Series)
Liver, reference fish 2 (Channel 1 source) vs. cadmium-fed fish 2 (Channel 2 source) (GSM197743_451.gpr raw data file attached to Series)
Liver, cadmium-fed fish 2 (Channel 1 source) vs. cadmium-injected fish 2 (Channel 2 source) (GSM197743_858.gpr raw data file attached to Series)
Liver, cadmium-injected fish 2 (Channel 1 source) vs. reference fish 2 (Channel 2 source) (GSM197743_458.gpr raw data file attached to Series)
Liver, reference fish 3 (Channel 1 source) vs. cadmium-injected fish 3 (Channel 2 source) (GSM197743_479.gpr raw data file attached to Series)
Liver, cadmium-fed fish 3 (Channel 1 source) vs. reference fish 3 (Channel 2 source) (GSM197743_481.gpr raw data file attached to Series)
Liver, cadmium-injected fish 3 (Channel 1 source) vs. cadmium-fed fish 3 (Channel 2 source) (GSM197743_441.gpr raw data file attached to Series)


title: Spores_germination following 2 hours of pre-incubation in nitrogen_1 hour and 30 minutes

description: S. cerevisiae spores pre-incubated in glucose, 1 hour and 30 minutes after the transfer to YPD


title: Spores_germination following 2 hours of pre-incubation in nitrogen_2 hours

description: S. cerevisiae spores pre-incubated in glucose, 2 hours after the transfer to YPD


title: Spores_germination following 2 hours of pre-incubation in glucose_1 hour

source_name: S. cerevisiae spores pre-incubated in glucose, 1 hour after the transfer to YPD


title: Spores_germination following 2 hours of pre-incubation in glucose_2 hours

source_name: S. cerevisiae spores pre-incubated in glucose, 2 hours after the transfer to YPD


title: Spores_germination following 2 hours of pre-incubation in glucose_2 hours and 30 minutes

source_name: S. cerevisiae spores pre-incubated in glucose, 2 hours and 30 minutes after the transfer to YPD


title: ENCODE Spike-In, Yale Group  Sample 2

type: mixed

first: Guoneng

last: Zhong

address: 300 George St

institute: Yale Med

description:
Red Channel: "ENCODE spike", 5 ug
Green Channel:  "ENCODE control", 5 ug

hyb_protocol: The labeled simulated "ChIP DNA" was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen).  Arrays were hybridized in Maui hybridization stations for 16-18h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: value = log_2(Signal for Cy5 / Signal for Cy3)

source_name: ENCODE Spike, Undiluted

label_protocol: 5 ug DNA was directly labeled by Klenow (New England Biolabs), random priming with Cy5-coupled nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Sample received as part of the ENCODE consortium "ENCODE Spike 77 ng/ul, Undiluted"

tag: Cloned promoter sequences

source_name: Control for ENCODE Spike

label_protocol: 5 ug DNA was directly labeled by Klenow (New England Biolabs), random priming with Cy3-coupled nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Sample received as part of the ENCODE consortium "ENCODE Control 200 ng/ul"

tag: Sheared genomic DNA


title: Spores_germination following 2 hours of pre-incubation in glucose_4 hours

source_name: S. cerevisiae spores pre-incubated in glucose, 4 hours after the transfer to YPD


title: Spores_incubation in nitrogen_6 hours

description: S. cerevisiae spores, 6 hours after the transfer to nitrogen


title: Spores_germination following 2 hours of pre-incubation in glucose_30 minutes

source_name: S. cerevisiae spores pre-incubated in glucose, 30 minutes after the transfer to YPD


title: Spores_germination following 2 hours of pre-incubation in glucose_3 hours

description: S. cerevisiae spores pre-incubated in glucose, 3 hours after the transfer to YPD


title: Spores_germination following 2 hours of pre-incubation in glucose_3 hours and 30 minutes

source_name: S. cerevisiae spores pre-incubated in glucose, 3 hours and 30 minutes after the transfer to YPD


title: HOXA13 ChIP (HG18 Array 2 of 2)

description: HG18 Array 1 of 2

source_name: HOXA13 ChIP

source_name: Mock ChIP of Rabbit IGG


title: Spores_incubation in nitrogen_4 hours and 30 minutes

description: S. cerevisiae spores, 4 hours and 30 minutes after the transfer to nitrogen


title: ENCODE Spike-In, Yale Group  Sample 3


title: Spores_germination following 2 hours of pre-incubation in glucose_1 hour and 30 minutes

source_name: S. cerevisiae spores pre-incubated in glucose, 1 hour and 30 minutes after the transfer to YPD


title: Spores_incubation in nitrogen_3 hours

description: S. cerevisiae spores, 3 hours after the transfer to nitrogen


title: Spores_incubation in nitrogen_2 hours and 30 minutes

description: S. cerevisiae spores, 2 hours and 30 minutes after the transfer to nitrogen


title: Spores_incubation in nitrogen_2 hours

description: S. cerevisiae spores, 2 hours after the transfer to nitrogen


title: Spores_incubation in nitrogen_1 hour

description: S. cerevisiae spores, 1 hour after the transfer to nitrogen


title: Spores_incubation in nitrogen_45 minutes

description: S. cerevisiae spores, 45 minutes after the transfer to nitrogen


title: Spores_incubation in nitrogen_1 hour and 30 minutes

description: S. cerevisiae spores, 1 hour and 30 minutes after the transfer to nitrogen


title: ENCODE Spike-In, Yale Group  Sample 1


title: Spores_incubation in nitrogen_3 hours and 30 minutes

description: S. cerevisiae spores, 3 hours and 30 minutes after the transfer to nitrogen


title: Spores_incubation in nitrogen_30 minutes

description: S. cerevisiae spores, 30 minutes after the transfer to nitrogen


title: Spores_incubation in glucose_3 hours and 30 minutes

description: S. cerevisiae spores, 3 hours and 30 minutes after the transfer to glucose


title: Spores_incubation in glucose_3 hours

description: S. cerevisiae spores, 3 hours after the transfer to glucose


title: Spores_incubation in glucose_6 hours

description: S. cerevisiae spores, 6 hours after the transfer to glucose


title: Spores_incubation in nitrogen_15 minutes

description: S. cerevisiae spores, 15 minutes after the transfer to nitrogen


title: Spores_incubation in glucose_1 hour

description: S. cerevisiae spores, 1 hour after the transfer to glucose


title: Spores_incubation in glucose_2 hours

description: S. cerevisiae spores, 2 hours after the transfer to glucose


title: Spores_incubation in glucose_1 hour and 30 minutes

description: S. cerevisiae spores, 1 hour and 30 minutes after the transfer to glucose


title: Spores_incubation in glucose_45 minutes

description: S. cerevisiae spores, 45 minutes after the transfer to glucose


title: Spores_incubation in glucose_2 hours and 30 minutes

description: S. cerevisiae spores, 2 hours and 30 minutes after the transfer to glucose


title: Spores_incubation in glucose_30 minutes

description: S. cerevisiae spores, 30 minutes after the transfer to glucose


title: Spores_incubation in glucose_4 hours

description: S. cerevisiae spores, 4 hours after the transfer to glucose


title: Spore germination_6 hours and 30 minutes

description: S. cerevisiae spores, 6 hours and 30 minutes after the transfer to YPD

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using ScanArray 4000 scanner (Packard BioScience) and image intensity data were extracted and analyzed with QuantArray analysis software.

data_processing: For each array, bad spots were omitted from the analysis. For each spot, the Quantarray program outputs the level of signal intensity and background fluorescence. As a first step, we re-defined the spot intensity by subtracting the spot-specific background. For each channel (Cy3 or Cy5) we then calculated the value of background signal, defined by the mean (intensity-background) of the controlled spots printed with 3x SSC buffer. All intensity values below this background level were reset to this background level. The data for each spot was then transformed into a log2-ratios. The data was normalized by subtracting from each log2ratio the median. Values of duplicates were averaged.


title: Spore germination_6 hours and 45 minutes

description: S. cerevisiae spores, 6 hours and 45 minutes after the transfer to YPD


title: Spores_incubation in glucose_15 minutes

description: S. cerevisiae spores, 15 minutes after the transfer to glucose


title: Spore germination_7 hours and 30 minutes

description: S. cerevisiae spores, 7 hours and 30 minutes after the transfer to YPD


title: Spore germination_7 hours and 15 minutes

description: S. cerevisiae spores, 7 hours and 15 minutes after the transfer to YPD


title: Spore germination_5 hours and 45 minutes

description: S. cerevisiae spores, 5 hours and 45 minutes after the transfer to YPD