title: Female 2 chip B

description:
Goal of experimet: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice. (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference)
Whole spleen was taken from pre-lupus (4 months old) BWF1 (females are lupus-prone) male and female mice
Preparation of cDNA.  Double-stranded cDNA was synthesized from purified RNA.  The first strand was synthesized by incubating 5 μg of RNA with 100 pg/ml T7-(dT)24 primer (HPLC purified DNA primer sequence: 5’-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGG-(dT)24 -3’ Genset Corp, San Diego, CA) at 70°C for 10 minutes.  Samples were incubated for 1 hour at 42°C with the following mix: 1X first strand buffer, 10 mM dithiothreitol, 500 μM each dNTP, 200 U SuperScript II in diethylpyrocarbonate (DEPC)-treated water up to 20 μl.  Second strand synthesis was performed by incubating the first strand with the following mix for 2 hours at 16°C: 1X second strand reaction buffer, 200 μM dntps, 10 U E. coli DNA ligase, 40 U E coli DNA Polymerase I, 2 U of E. coli RNase H up to 150 μl with DEPC-treated water (all reagents were contained in SuperScript Choice System for cDNA Synthesis, Invitrogen).  A phenol/chloroform extraction was performed on the ds-cDNA preparation before biotin-labeled cRNA was generated.
Synthesis and fragmentation of biotin-labeled cRNA (in vitro transcription). The ENZO BioArrayTM HighYieldTM RNA Transcript Labeling Kit (T7) (Enzo diagnostics, Inc., Farmingdale, NY) was used to produce large amounts of hybridizable biotin-labeled RNA targets by in vitro transcription from the ds-cDNA.  The following mix was incubated at 37°C for 5 hours:  1 μg of ds-cDNA, 1X HY reaction buffer, 1X biotin labeled ribonucleotides, 1X dithiothreitol, 1X T7 RNA Polymerase.  Biotin-labeled cRNA was run over RNeasy spin columns (Qiagen), quantified, and run on an agarose gel to visualize the size distribution of labeled transcripts.  Twenty micrograms of cRNA was incubated with 1X fragmentation buffer for 35 minutes at 94°C.  (5X fragmentation buffer: 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc).  After fragmentation, the samples were stored at -20°C until the hybridization was performed.
Sample hybridization.  Oligonucleotide microarrays (MGU74v2 A, B, and C GeneChip probe arrays; Affymetrix) were hybridized with labeled cRNA derived from spleens from individual mice.  For each array,15 μg of fragmented cRNA was mixed with a hybridization cocktail consisting of 1X hybridization buffer (2X hybridization buffer: 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween), 0.5 mg/ml acetylated BSA (Invitrogen),  0.1 mg/ml herring sperm DNA (Promega), and water (BioWhittaker) up to 300 μl).  Biotin labeled cRNA transcripts of the E. coli and P1 bacteriophage genes, BioB, bioC, bioD, and cre (GeneChip Eukaryotic Hybridization control kit, Affymetrix) were spiked into each hybridization mix at 1.5, 5, 25, and 100 pM to evaluate sample hybridization efficiency for each array. The hybridization cocktail was heated to 99°C and then 45°C for 5 minutes each before it was centrifuged to remove any insoluble material. The array was equilibrated to room temperature, moistened with 1X hybridization buffer, and incubated for 10 minutes at 45°C with rotation.  After incubation, the buffer solution was removed from the array. The array was filled with 300 μl of the hybridization cocktail, placed in a rotisserie box in a 45°C oven, and incubated for 16 hours while rotating at 60 rpm.
Washing and staining of array.  The hybridization cocktail was removed and the GeneChip Fluidics Station 400 (Affymetrix) with Microarray Suite software (Affymetrix) was used to wash and stain the probe arrays with the following protocol: 10 cycles of 2 mixes/cycle with wash buffer A at 25°C, 4 cycles of 15 mixes/cycle with wash buffer B at 50°C, 30 minute incubation with staining solution at 25°C, 10 cycles of 4 mixes/cycle with wash buffer A at 25°C.  Wash buffer A -- non-stringent wash buffer (6X sodium chloride sodium phosphate + ethylenediaminetetraacetic acid (SSPE), 0.01% Tween-20).  (20X SSPE: 3 M NaCl, 0.2 M NaH2PO4, 0.02 EDTA) (BioWhittaker).  Wash buffer B – stringent wash buffer (100mM MES, 0.1 M [Na+], 0.1% Tween 20).  Staining solution (1X 2-(N-Morpholino)ethanesulfonic Acid (MES) stain buffer, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin (SAPE), and water up to 600 μl). (12X MES stain buffer: 1.22 M MES, 0.89 M [Na+]).
Analysis.  After staining, the probe arrays were scanned using the GeneChip 3000 Scanner (Affymetrix) with Microarray Suite software (Affymetrix).  Technical and assay variation between arrays was corrected for by multiplying or dividing the overall intensity of each array by a scaling factor so that the overall intensity of each array was equivalent to facilitate comparison analysis.


title: female 3 chip C

status: Public on Aug 23 2005

type: RNA

city: Denver

first: Melanie

last: Gubbels

state: CO

country: USA

institute: University of Colorado Health Sciences Center

description:
Goal of experiment: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice. (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference). Whole spleen was taken from pre-lupus (4 months old) BWF1 (females are lupus-prone) male and female mice.  Preparation of cDNA.  Double-stranded cDNA was synthesized from purified RNA.  The first strand was synthesized by incubating 5 μg of RNA with 100 pg/ml T7-(dT)24 primer (HPLC purified DNA primer sequence: 5’-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGG-(dT)24 -3’ Genset Corp, San Diego, CA) at 70°C for 10 minutes.  Samples were incubated for 1 hour at 42°C with the following mix: 1X first strand buffer, 10 mM dithiothreitol, 500 μM each dNTP, 200 U SuperScript II in diethylpyrocarbonate (DEPC)-treated water up to 20 μl.  Second strand synthesis was performed by incubating the first strand with the following mix for 2 hours at 16°C: 1X second strand reaction buffer, 200 μM dntps, 10 U E. coli DNA ligase, 40 U E coli DNA Polymerase I, 2 U of E. coli RNase H up to 150 μl with DEPC-treated water (all reagents were contained in SuperScript Choice System for cDNA Synthesis, Invitrogen).  A phenol/chloroform extraction was performed on the ds-cDNA preparation before biotin-labeled cRNA was generated.
Synthesis and fragmentation of biotin-labeled cRNA (in vitro transcription). The ENZO BioArrayTM HighYieldTM RNA Transcript Labeling Kit (T7) (Enzo diagnostics, Inc., Farmingdale, NY) was used to produce large amounts of hybridizable biotin-labeled RNA targets by in vitro transcription from the ds-cDNA.  The following mix was incubated at 37°C for 5 hours:  1 μg of ds-cDNA, 1X HY reaction buffer, 1X biotin labeled ribonucleotides, 1X dithiothreitol, 1X T7 RNA Polymerase.  Biotin-labeled cRNA was run over RNeasy spin columns (Qiagen), quantified, and run on an agarose gel to visualize the size distribution of labeled transcripts.  Twenty micrograms of cRNA was incubated with 1X fragmentation buffer for 35 minutes at 94°C.  (5X fragmentation buffer: 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc).  After fragmentation, the samples were stored at -20°C until the hybridization was performed.
Sample hybridization.  Oligonucleotide microarrays (MGU74v2 A, B, and C GeneChip probe arrays; Affymetrix) were hybridized with labeled cRNA derived from spleens from individual mice.  For each array,15 μg of fragmented cRNA was mixed with a hybridization cocktail consisting of 1X hybridization buffer (2X hybridization buffer: 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween), 0.5 mg/ml acetylated BSA (Invitrogen),  0.1 mg/ml herring sperm DNA (Promega), and water (BioWhittaker) up to 300 μl).  Biotin labeled cRNA transcripts of the E. coli and P1 bacteriophage genes, BioB, bioC, bioD, and cre (GeneChip Eukaryotic Hybridization control kit, Affymetrix) were spiked into each hybridization mix at 1.5, 5, 25, and 100 pM to evaluate sample hybridization efficiency for each array. The hybridization cocktail was heated to 99°C and then 45°C for 5 minutes each before it was centrifuged to remove any insoluble material. The array was equilibrated to room temperature, moistened with 1X hybridization buffer, and incubated for 10 minutes at 45°C with rotation.  After incubation, the buffer solution was removed from the array. The array was filled with 300 μl of the hybridization cocktail, placed in a rotisserie box in a 45°C oven, and incubated for 16 hours while rotating at 60 rpm.
Washing and staining of array.  The hybridization cocktail was removed and the GeneChip Fluidics Station 400 (Affymetrix) with Microarray Suite software (Affymetrix) was used to wash and stain the probe arrays with the following protocol: 10 cycles of 2 mixes/cycle with wash buffer A at 25°C, 4 cycles of 15 mixes/cycle with wash buffer B at 50°C, 30 minute incubation with staining solution at 25°C, 10 cycles of 4 mixes/cycle with wash buffer A at 25°C.  Wash buffer A -- non-stringent wash buffer (6X sodium chloride sodium phosphate + ethylenediaminetetraacetic acid (SSPE), 0.01% Tween-20).  (20X SSPE: 3 M NaCl, 0.2 M NaH2PO4, 0.02 EDTA) (BioWhittaker).  Wash buffer B – stringent wash buffer (100mM MES, 0.1 M [Na+], 0.1% Tween 20).  Staining solution (1X 2-(N-Morpholino)ethanesulfonic Acid (MES) stain buffer, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin (SAPE), and water up to 600 μl). (12X MES stain buffer: 1.22 M MES, 0.89 M [Na+]).
Analysis.  After staining, the probe arrays were scanned using the GeneChip 3000 Scanner (Affymetrix) with Microarray Suite software (Affymetrix).  Technical and assay variation between arrays was corrected for by multiplying or dividing the overall intensity of each array by a scaling factor so that the overall intensity of each array was equivalent to facilitate comparison analysis.

Keywords = disease-prone (female) vs not disease prone (male)

molecule: total RNA

organism: Mus musculus

source_name: Whole spleen taken at 4 months of age


title: male 4 chip B

description:
Goal of experimet: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice. (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference). Whole spleen was taken from pre-lupus (4 months old) BWF1 (females are lupus-prone) male and female mice. Preparation of cDNA.  Double-stranded cDNA was synthesized from purified RNA.  The first strand was synthesized by incubating 5 μg of RNA with 100 pg/ml T7-(dT)24 primer (HPLC purified DNA primer sequence: 5’-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGG-(dT)24 -3’ Genset Corp, San Diego, CA) at 70°C for 10 minutes.  Samples were incubated for 1 hour at 42°C with the following mix: 1X first strand buffer, 10 mM dithiothreitol, 500 μM each dNTP, 200 U SuperScript II in diethylpyrocarbonate (DEPC)-treated water up to 20 μl.  Second strand synthesis was performed by incubating the first strand with the following mix for 2 hours at 16°C: 1X second strand reaction buffer, 200 μM dntps, 10 U E. coli DNA ligase, 40 U E coli DNA Polymerase I, 2 U of E. coli RNase H up to 150 μl with DEPC-treated water (all reagents were contained in SuperScript Choice System for cDNA Synthesis, Invitrogen).  A phenol/chloroform extraction was performed on the ds-cDNA preparation before biotin-labeled cRNA was generated.
Synthesis and fragmentation of biotin-labeled cRNA (in vitro transcription). The ENZO BioArrayTM HighYieldTM RNA Transcript Labeling Kit (T7) (Enzo diagnostics, Inc., Farmingdale, NY) was used to produce large amounts of hybridizable biotin-labeled RNA targets by in vitro transcription from the ds-cDNA.  The following mix was incubated at 37°C for 5 hours:  1 μg of ds-cDNA, 1X HY reaction buffer, 1X biotin labeled ribonucleotides, 1X dithiothreitol, 1X T7 RNA Polymerase.  Biotin-labeled cRNA was run over RNeasy spin columns (Qiagen), quantified, and run on an agarose gel to visualize the size distribution of labeled transcripts.  Twenty micrograms of cRNA was incubated with 1X fragmentation buffer for 35 minutes at 94°C.  (5X fragmentation buffer: 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc).  After fragmentation, the samples were stored at -20°C until the hybridization was performed.
Sample hybridization.  Oligonucleotide microarrays (MGU74v2 A, B, and C GeneChip probe arrays; Affymetrix) were hybridized with labeled cRNA derived from spleens from individual mice.  For each array,15 μg of fragmented cRNA was mixed with a hybridization cocktail consisting of 1X hybridization buffer (2X hybridization buffer: 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween), 0.5 mg/ml acetylated BSA (Invitrogen),  0.1 mg/ml herring sperm DNA (Promega), and water (BioWhittaker) up to 300 μl).  Biotin labeled cRNA transcripts of the E. coli and P1 bacteriophage genes, BioB, bioC, bioD, and cre (GeneChip Eukaryotic Hybridization control kit, Affymetrix) were spiked into each hybridization mix at 1.5, 5, 25, and 100 pM to evaluate sample hybridization efficiency for each array. The hybridization cocktail was heated to 99°C and then 45°C for 5 minutes each before it was centrifuged to remove any insoluble material. The array was equilibrated to room temperature, moistened with 1X hybridization buffer, and incubated for 10 minutes at 45°C with rotation.  After incubation, the buffer solution was removed from the array. The array was filled with 300 μl of the hybridization cocktail, placed in a rotisserie box in a 45°C oven, and incubated for 16 hours while rotating at 60 rpm.
Washing and staining of array.  The hybridization cocktail was removed and the GeneChip Fluidics Station 400 (Affymetrix) with Microarray Suite software (Affymetrix) was used to wash and stain the probe arrays with the following protocol: 10 cycles of 2 mixes/cycle with wash buffer A at 25°C, 4 cycles of 15 mixes/cycle with wash buffer B at 50°C, 30 minute incubation with staining solution at 25°C, 10 cycles of 4 mixes/cycle with wash buffer A at 25°C.  Wash buffer A -- non-stringent wash buffer (6X sodium chloride sodium phosphate + ethylenediaminetetraacetic acid (SSPE), 0.01% Tween-20).  (20X SSPE: 3 M NaCl, 0.2 M NaH2PO4, 0.02 EDTA) (BioWhittaker).  Wash buffer B – stringent wash buffer (100mM MES, 0.1 M [Na+], 0.1% Tween 20).  Staining solution (1X 2-(N-Morpholino)ethanesulfonic Acid (MES) stain buffer, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin (SAPE), and water up to 600 μl). (12X MES stain buffer: 1.22 M MES, 0.89 M [Na+]).
Analysis.  After staining, the probe arrays were scanned using the GeneChip 3000 Scanner (Affymetrix) with Microarray Suite software (Affymetrix).  Technical and assay variation between arrays was corrected for by multiplying or dividing the overall intensity of each array by a scaling factor so that the overall intensity of each array was equivalent to facilitate comparison analysis.
Keywords = disease-prone (female) vs not disease prone (male)


title: Female 4 chip C

description:
Goal of experiment: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice. (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference). Whole spleen was taken from pre-lupus (4 months old) BWF1 (females are lupus-prone) male and female mice.  Preparation of cDNA.  Double-stranded cDNA was synthesized from purified RNA.  The first strand was synthesized by incubating 5 μg of RNA with 100 pg/ml T7-(dT)24 primer (HPLC purified DNA primer sequence: 5’-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGG-(dT)24 -3’ Genset Corp, San Diego, CA) at 70°C for 10 minutes.  Samples were incubated for 1 hour at 42°C with the following mix: 1X first strand buffer, 10 mM dithiothreitol, 500 μM each dNTP, 200 U SuperScript II in diethylpyrocarbonate (DEPC)-treated water up to 20 μl.  Second strand synthesis was performed by incubating the first strand with the following mix for 2 hours at 16°C: 1X second strand reaction buffer, 200 μM dntps, 10 U E. coli DNA ligase, 40 U E coli DNA Polymerase I, 2 U of E. coli RNase H up to 150 μl with DEPC-treated water (all reagents were contained in SuperScript Choice System for cDNA Synthesis, Invitrogen).  A phenol/chloroform extraction was performed on the ds-cDNA preparation before biotin-labeled cRNA was generated.  Synthesis and fragmentation of biotin-labeled cRNA (in vitro transcription). The ENZO BioArrayTM HighYieldTM RNA Transcript Labeling Kit (T7) (Enzo diagnostics, Inc., Farmingdale, NY) was used to produce large amounts of hybridizable biotin-labeled RNA targets by in vitro transcription from the ds-cDNA.  The following mix was incubated at 37°C for 5 hours:  1 μg of ds-cDNA, 1X HY reaction buffer, 1X biotin labeled ribonucleotides, 1X dithiothreitol, 1X T7 RNA Polymerase.  Biotin-labeled cRNA was run over RNeasy spin columns (Qiagen), quantified, and run on an agarose gel to visualize the size distribution of labeled transcripts.  Twenty micrograms of cRNA was incubated with 1X fragmentation buffer for 35 minutes at 94°C.  (5X fragmentation buffer: 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc).  After fragmentation, the samples were stored at -20°C until the hybridization was performed.  Sample hybridization.  Oligonucleotide microarrays (MGU74v2 A, B, and C GeneChip probe arrays; Affymetrix) were hybridized with labeled cRNA derived from spleens from individual mice.  For each array,15 μg of fragmented cRNA was mixed with a hybridization cocktail consisting of 1X hybridization buffer (2X hybridization buffer: 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween), 0.5 mg/ml acetylated BSA (Invitrogen),  0.1 mg/ml herring sperm DNA (Promega), and water (BioWhittaker) up to 300 μl).  Biotin labeled cRNA transcripts of the E. coli and P1 bacteriophage genes, BioB, bioC, bioD, and cre (GeneChip Eukaryotic Hybridization control kit, Affymetrix) were spiked into each hybridization mix at 1.5, 5, 25, and 100 pM to evaluate sample hybridization efficiency for each array. The hybridization cocktail was heated to 99°C and then 45°C for 5 minutes each before it was centrifuged to remove any insoluble material. The array was equilibrated to room temperature, moistened with 1X hybridization buffer, and incubated for 10 minutes at 45°C with rotation.  After incubation, the buffer solution was removed from the array. The array was filled with 300 μl of the hybridization cocktail, placed in a rotisserie box in a 45°C oven, and incubated for 16 hours while rotating at 60 rpm.  Washing and staining of array.  The hybridization cocktail was removed and the GeneChip Fluidics Station 400 (Affymetrix) with Microarray Suite software (Affymetrix) was used to wash and stain the probe arrays with the following protocol: 10 cycles of 2 mixes/cycle with wash buffer A at 25°C, 4 cycles of 15 mixes/cycle with wash buffer B at 50°C, 30 minute incubation with staining solution at 25°C, 10 cycles of 4 mixes/cycle with wash buffer A at 25°C.  Wash buffer A -- non-stringent wash buffer (6X sodium chloride sodium phosphate + ethylenediaminetetraacetic acid (SSPE), 0.01% Tween-20).  (20X SSPE: 3 M NaCl, 0.2 M NaH2PO4, 0.02 EDTA) (BioWhittaker).  Wash buffer B – stringent wash buffer (100mM MES, 0.1 M [Na+], 0.1% Tween 20).  Staining solution (1X 2-(N-Morpholino)ethanesulfonic Acid (MES) stain buffer, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin (SAPE), and water up to 600 μl). (12X MES stain buffer: 1.22 M MES, 0.89 M [Na+]).  Analysis.  After staining, the probe arrays were scanned using the GeneChip 3000 Scanner (Affymetrix) with Microarray Suite software (Affymetrix).  Technical and assay variation between arrays was corrected for by multiplying or dividing the overall intensity of each array by a scaling factor so that the overall intensity of each array was equivalent to facilitate comparison analysis.
Keywords = disease-prone (female) vs not disease prone (male)


title: Female 1 chip B

description:
Goal of experimet: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice. (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference)Whole spleen was taken from pre-lupus (4 months old) BWF1 (females are lupus-prone) male and female micePreparation of cDNA.  Double-stranded cDNA was synthesized from purified RNA.  The first strand was synthesized by incubating 5 μg of RNA with 100 pg/ml T7-(dT)24 primer (HPLC purified DNA primer sequence: 5’-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGG-(dT)24 -3’ Genset Corp, San Diego, CA) at 70°C for 10 minutes.  Samples were incubated for 1 hour at 42°C with the following mix: 1X first strand buffer, 10 mM dithiothreitol, 500 μM each dNTP, 200 U SuperScript II in diethylpyrocarbonate (DEPC)-treated water up to 20 μl.  Second strand synthesis was performed by incubating the first strand with the following mix for 2 hours at 16°C: 1X second strand reaction buffer, 200 μM dntps, 10 U E. coli DNA ligase, 40 U E coli DNA Polymerase I, 2 U of E. coli RNase H up to 150 μl with DEPC-treated water (all reagents were contained in SuperScript Choice System for cDNA Synthesis, Invitrogen).  A phenol/chloroform extraction was performed on the ds-cDNA preparation before biotin-labeled cRNA was generated.
Synthesis and fragmentation of biotin-labeled cRNA (in vitro transcription). The ENZO BioArrayTM HighYieldTM RNA Transcript Labeling Kit (T7) (Enzo diagnostics, Inc., Farmingdale, NY) was used to produce large amounts of hybridizable biotin-labeled RNA targets by in vitro transcription from the ds-cDNA.  The following mix was incubated at 37°C for 5 hours:  1 μg of ds-cDNA, 1X HY reaction buffer, 1X biotin labeled ribonucleotides, 1X dithiothreitol, 1X T7 RNA Polymerase.  Biotin-labeled cRNA was run over RNeasy spin columns (Qiagen), quantified, and run on an agarose gel to visualize the size distribution of labeled transcripts.  Twenty micrograms of cRNA was incubated with 1X fragmentation buffer for 35 minutes at 94°C.  (5X fragmentation buffer: 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc).  After fragmentation, the samples were stored at -20°C until the hybridization was performed.
Sample hybridization.  Oligonucleotide microarrays (MGU74v2 A, B, and C GeneChip probe arrays; Affymetrix) were hybridized with labeled cRNA derived from spleens from individual mice.  For each array,15 μg of fragmented cRNA was mixed with a hybridization cocktail consisting of 1X hybridization buffer (2X hybridization buffer: 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween), 0.5 mg/ml acetylated BSA (Invitrogen),  0.1 mg/ml herring sperm DNA (Promega), and water (BioWhittaker) up to 300 μl).  Biotin labeled cRNA transcripts of the E. coli and P1 bacteriophage genes, BioB, bioC, bioD, and cre (GeneChip Eukaryotic Hybridization control kit, Affymetrix) were spiked into each hybridization mix at 1.5, 5, 25, and 100 pM to evaluate sample hybridization efficiency for each array. The hybridization cocktail was heated to 99°C and then 45°C for 5 minutes each before it was centrifuged to remove any insoluble material. The array was equilibrated to room temperature, moistened with 1X hybridization buffer, and incubated for 10 minutes at 45°C with rotation.  After incubation, the buffer solution was removed from the array. The array was filled with 300 μl of the hybridization cocktail, placed in a rotisserie box in a 45°C oven, and incubated for 16 hours while rotating at 60 rpm.
Washing and staining of array.  The hybridization cocktail was removed and the GeneChip Fluidics Station 400 (Affymetrix) with Microarray Suite software (Affymetrix) was used to wash and stain the probe arrays with the following protocol: 10 cycles of 2 mixes/cycle with wash buffer A at 25°C, 4 cycles of 15 mixes/cycle with wash buffer B at 50°C, 30 minute incubation with staining solution at 25°C, 10 cycles of 4 mixes/cycle with wash buffer A at 25°C.  Wash buffer A -- non-stringent wash buffer (6X sodium chloride sodium phosphate + ethylenediaminetetraacetic acid (SSPE), 0.01% Tween-20).  (20X SSPE: 3 M NaCl, 0.2 M NaH2PO4, 0.02 EDTA) (BioWhittaker).  Wash buffer B – stringent wash buffer (100mM MES, 0.1 M [Na+], 0.1% Tween 20).  Staining solution (1X 2-(N-Morpholino)ethanesulfonic Acid (MES) stain buffer, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin (SAPE), and water up to 600 μl). (12X MES stain buffer: 1.22 M MES, 0.89 M [Na+]).
Analysis.  After staining, the probe arrays were scanned using the GeneChip 3000 Scanner (Affymetrix) with Microarray Suite software (Affymetrix).  Technical and assay variation between arrays was corrected for by multiplying or dividing the overall intensity of each array by a scaling factor so that the overall intensity of each array was equivalent to facilitate comparison analysis.

Keywords = disease-prone (female) vs not disease prone (male)


title: Male 3 chip B

description:
Goal of experimet: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice. (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference)Whole spleen was taken from pre-lupus (4 months old) BWF1 (females are lupus-prone) male and female mice
Preparation of cDNA.  Double-stranded cDNA was synthesized from purified RNA.  The first strand was synthesized by incubating 5 μg of RNA with 100 pg/ml T7-(dT)24 primer (HPLC purified DNA primer sequence: 5’-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGG-(dT)24 -3’ Genset Corp, San Diego, CA) at 70°C for 10 minutes.  Samples were incubated for 1 hour at 42°C with the following mix: 1X first strand buffer, 10 mM dithiothreitol, 500 μM each dNTP, 200 U SuperScript II in diethylpyrocarbonate (DEPC)-treated water up to 20 μl.  Second strand synthesis was performed by incubating the first strand with the following mix for 2 hours at 16°C: 1X second strand reaction buffer, 200 μM dntps, 10 U E. coli DNA ligase, 40 U E coli DNA Polymerase I, 2 U of E. coli RNase H up to 150 μl with DEPC-treated water (all reagents were contained in SuperScript Choice System for cDNA Synthesis, Invitrogen).  A phenol/chloroform extraction was performed on the ds-cDNA preparation before biotin-labeled cRNA was generated.
Synthesis and fragmentation of biotin-labeled cRNA (in vitro transcription). The ENZO BioArrayTM HighYieldTM RNA Transcript Labeling Kit (T7) (Enzo diagnostics, Inc., Farmingdale, NY) was used to produce large amounts of hybridizable biotin-labeled RNA targets by in vitro transcription from the ds-cDNA.  The following mix was incubated at 37°C for 5 hours:  1 μg of ds-cDNA, 1X HY reaction buffer, 1X biotin labeled ribonucleotides, 1X dithiothreitol, 1X T7 RNA Polymerase.  Biotin-labeled cRNA was run over RNeasy spin columns (Qiagen), quantified, and run on an agarose gel to visualize the size distribution of labeled transcripts.  Twenty micrograms of cRNA was incubated with 1X fragmentation buffer for 35 minutes at 94°C.  (5X fragmentation buffer: 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc).  After fragmentation, the samples were stored at -20°C until the hybridization was performed.
Sample hybridization.  Oligonucleotide microarrays (MGU74v2 A, B, and C GeneChip probe arrays; Affymetrix) were hybridized with labeled cRNA derived from spleens from individual mice.  For each array,15 μg of fragmented cRNA was mixed with a hybridization cocktail consisting of 1X hybridization buffer (2X hybridization buffer: 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween), 0.5 mg/ml acetylated BSA (Invitrogen),  0.1 mg/ml herring sperm DNA (Promega), and water (BioWhittaker) up to 300 μl).  Biotin labeled cRNA transcripts of the E. coli and P1 bacteriophage genes, BioB, bioC, bioD, and cre (GeneChip Eukaryotic Hybridization control kit, Affymetrix) were spiked into each hybridization mix at 1.5, 5, 25, and 100 pM to evaluate sample hybridization efficiency for each array. The hybridization cocktail was heated to 99°C and then 45°C for 5 minutes each before it was centrifuged to remove any insoluble material. The array was equilibrated to room temperature, moistened with 1X hybridization buffer, and incubated for 10 minutes at 45°C with rotation.  After incubation, the buffer solution was removed from the array. The array was filled with 300 μl of the hybridization cocktail, placed in a rotisserie box in a 45°C oven, and incubated for 16 hours while rotating at 60 rpm.
Washing and staining of array.  The hybridization cocktail was removed and the GeneChip Fluidics Station 400 (Affymetrix) with Microarray Suite software (Affymetrix) was used to wash and stain the probe arrays with the following protocol: 10 cycles of 2 mixes/cycle with wash buffer A at 25°C, 4 cycles of 15 mixes/cycle with wash buffer B at 50°C, 30 minute incubation with staining solution at 25°C, 10 cycles of 4 mixes/cycle with wash buffer A at 25°C.  Wash buffer A -- non-stringent wash buffer (6X sodium chloride sodium phosphate + ethylenediaminetetraacetic acid (SSPE), 0.01% Tween-20).  (20X SSPE: 3 M NaCl, 0.2 M NaH2PO4, 0.02 EDTA) (BioWhittaker).  Wash buffer B – stringent wash buffer (100mM MES, 0.1 M [Na+], 0.1% Tween 20).  Staining solution (1X 2-(N-Morpholino)ethanesulfonic Acid (MES) stain buffer, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin (SAPE), and water up to 600 μl). (12X MES stain buffer: 1.22 M MES, 0.89 M [Na+]).
Analysis.  After staining, the probe arrays were scanned using the GeneChip 3000 Scanner (Affymetrix) with Microarray Suite software (Affymetrix).  Technical and assay variation between arrays was corrected for by multiplying or dividing the overall intensity of each array by a scaling factor so that the overall intensity of each array was equivalent to facilitate comparison analysis.

Keywords = disease-prone (female) vs not disease prone (male)


title: Male 2 chip B

description:
Goal of experimet: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice. (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference)
Whole spleen was taken from pre-lupus (4 months old) BWF1 (females are lupus-prone) male and female mice
Preparation of cDNA.  Double-stranded cDNA was synthesized from purified RNA.  The first strand was synthesized by incubating 5 μg of RNA with 100 pg/ml T7-(dT)24 primer (HPLC purified DNA primer sequence: 5’-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGG-(dT)24 -3’ Genset Corp, San Diego, CA) at 70°C for 10 minutes.  Samples were incubated for 1 hour at 42°C with the following mix: 1X first strand buffer, 10 mM dithiothreitol, 500 μM each dNTP, 200 U SuperScript II in diethylpyrocarbonate (DEPC)-treated water up to 20 μl.  Second strand synthesis was performed by incubating the first strand with the following mix for 2 hours at 16°C: 1X second strand reaction buffer, 200 μM dntps, 10 U E. coli DNA ligase, 40 U E coli DNA Polymerase I, 2 U of E. coli RNase H up to 150 μl with DEPC-treated water (all reagents were contained in SuperScript Choice System for cDNA Synthesis, Invitrogen).  A phenol/chloroform extraction was performed on the ds-cDNA preparation before biotin-labeled cRNA was generated.
Synthesis and fragmentation of biotin-labeled cRNA (in vitro transcription). The ENZO BioArrayTM HighYieldTM RNA Transcript Labeling Kit (T7) (Enzo diagnostics, Inc., Farmingdale, NY) was used to produce large amounts of hybridizable biotin-labeled RNA targets by in vitro transcription from the ds-cDNA.  The following mix was incubated at 37°C for 5 hours:  1 μg of ds-cDNA, 1X HY reaction buffer, 1X biotin labeled ribonucleotides, 1X dithiothreitol, 1X T7 RNA Polymerase.  Biotin-labeled cRNA was run over RNeasy spin columns (Qiagen), quantified, and run on an agarose gel to visualize the size distribution of labeled transcripts.  Twenty micrograms of cRNA was incubated with 1X fragmentation buffer for 35 minutes at 94°C.  (5X fragmentation buffer: 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc).  After fragmentation, the samples were stored at -20°C until the hybridization was performed.
Sample hybridization.  Oligonucleotide microarrays (MGU74v2 A, B, and C GeneChip probe arrays; Affymetrix) were hybridized with labeled cRNA derived from spleens from individual mice.  For each array,15 μg of fragmented cRNA was mixed with a hybridization cocktail consisting of 1X hybridization buffer (2X hybridization buffer: 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween), 0.5 mg/ml acetylated BSA (Invitrogen),  0.1 mg/ml herring sperm DNA (Promega), and water (BioWhittaker) up to 300 μl).  Biotin labeled cRNA transcripts of the E. coli and P1 bacteriophage genes, BioB, bioC, bioD, and cre (GeneChip Eukaryotic Hybridization control kit, Affymetrix) were spiked into each hybridization mix at 1.5, 5, 25, and 100 pM to evaluate sample hybridization efficiency for each array. The hybridization cocktail was heated to 99°C and then 45°C for 5 minutes each before it was centrifuged to remove any insoluble material. The array was equilibrated to room temperature, moistened with 1X hybridization buffer, and incubated for 10 minutes at 45°C with rotation.  After incubation, the buffer solution was removed from the array. The array was filled with 300 μl of the hybridization cocktail, placed in a rotisserie box in a 45°C oven, and incubated for 16 hours while rotating at 60 rpm.
Washing and staining of array.  The hybridization cocktail was removed and the GeneChip Fluidics Station 400 (Affymetrix) with Microarray Suite software (Affymetrix) was used to wash and stain the probe arrays with the following protocol: 10 cycles of 2 mixes/cycle with wash buffer A at 25°C, 4 cycles of 15 mixes/cycle with wash buffer B at 50°C, 30 minute incubation with staining solution at 25°C, 10 cycles of 4 mixes/cycle with wash buffer A at 25°C.  Wash buffer A -- non-stringent wash buffer (6X sodium chloride sodium phosphate + ethylenediaminetetraacetic acid (SSPE), 0.01% Tween-20).  (20X SSPE: 3 M NaCl, 0.2 M NaH2PO4, 0.02 EDTA) (BioWhittaker).  Wash buffer B – stringent wash buffer (100mM MES, 0.1 M [Na+], 0.1% Tween 20).  Staining solution (1X 2-(N-Morpholino)ethanesulfonic Acid (MES) stain buffer, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin (SAPE), and water up to 600 μl). (12X MES stain buffer: 1.22 M MES, 0.89 M [Na+]).
Analysis.  After staining, the probe arrays were scanned using the GeneChip 3000 Scanner (Affymetrix) with Microarray Suite software (Affymetrix).  Technical and assay variation between arrays was corrected for by multiplying or dividing the overall intensity of each array by a scaling factor so that the overall intensity of each array was equivalent to facilitate comparison analysis.

Keywords = disease-prone (female) vs not disease prone (male)


title: AD50 hpi 1

status: Public on Aug 25 2005

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31131.gif

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Homo sapiens

source_name: Mock

tag: Mock

source_name: AD169 50 hpi

tag: AD169 50 hpi


title: BalbC TraSH 3

status: Public on Aug 24 2005

description:
Simple annotation: Comparative genomics, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44319.gif

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: input

tag: input

source_name: output

tag: output


title: G6 ciliary body

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27741.gif

source_name: Stratagene Universal Human Reference 1 (Amp 7/12/01)

source_name: G6 ciliary body

tag: G6 ciliary body


title: G7 temporal retina

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27744.gif

tag: Stratagene Universal Human Reference 1 (Amp 7/12/01)

source_name: G7 temporal retina

tag: G7 temporal retina


title: G2 Macula (rep)

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs//23749.gif

source_name: G2 Macula (rep)

tag: G2 Macula (rep)


title: G6 iris

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27742.gif

source_name: G6 iris

tag: G6 iris


title: G7 nasal retina

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27743.gif

source_name: G7 nasal retina

tag: G7 nasal retina


title: G5 lens

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27671.gif

source_name: G5 lens

tag: G5 lens


title: G4 optic nerve

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27670.gif

source_name: G4 optic nerve

tag: G4 optic nerve


title: G5 ciliary body

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27739.gif

source_name: G5 ciliary body

tag: G5 ciliary body


title: G2 Inf. Retina (rep)

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs//23748.gif

source_name: G2 Inf. Retina (rep)

tag: G2 Inf. Retina (rep)


title: G4 cornea

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27669.gif

source_name: G4 cornea

tag: G4 cornea


title: G8 Retina

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24273.gif

source_name: G8 Retina

tag: G8 Retina


title: G1 optic nerve (rep1)

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs//27682.gif

source_name: G1 optic nerve (rep1)

tag: G1 optic nerve (rep1)


title: G2 Nasal Retina

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24276.gif

source_name: G2 Nasal Retina

tag: G2 Nasal Retina


title: G3 Iris

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24270.gif

source_name: G3 Iris

tag: G3 Iris


title: G7 optic nerve

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs//27679.gif

source_name: G7 optic nerve

tag: G7 optic nerve


title: G3 Macula

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23745.gif

source_name: G3 Macula

tag: G3 Macula


title: G5 nasal retina

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27738.gif

source_name: Stratagene Universal Human Reference 1 (Amp 7/12/01)

source_name: G5 nasal retina

tag: G5 nasal retina


title: G3 Sup. Retina

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23744.gif

tag: Stratagene Universal Human Reference 1 (Amp 7/12/01)

source_name: G3 Sup. Retina

tag: G3 Sup. Retina


title: G3 Ciliary Body

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23743.gif

source_name: G3 Ciliary Body

tag: G3 Ciliary Body


title: G6 lens

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs//27676.gif

source_name: G6 lens

tag: G6 lens


title: Brain (occipital)

description:
Simple annotation: Normal tissue, Brain
Image: http://smd.stanford.edu/MicroArray/gifs//27683.gif

source_name: Brain (occipital)

tag: Brain (occipital)


title: G7 cornea

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs//27678.gif

source_name: G7 cornea

tag: G7 cornea


title: G8 optic nerve

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27675.gif

source_name: G8 optic nerve

tag: G8 optic nerve


title: G2 Sup. Retina

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs//23747.gif

source_name: G2 Sup. Retina

tag: G2 Sup. Retina


title: G3 Nasal Retina

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24272.gif

source_name: G3 Nasal Retina

tag: G3 Nasal Retina


title: G6 cornea

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs//27677.gif

source_name: G6 cornea

tag: G6 cornea


title: G3 Temp. Retina

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24268.gif

source_name: G3 Temp. Retina

tag: G3 Temp. Retina


title: G7 macula

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs//27680.gif

source_name: G7 macula

tag: G7 macula


title: G4 lens

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27668.gif

source_name: G4 lens

tag: G4 lens


title: Brain (cerebellum)

description:
Simple annotation: Normal tissue, Brain
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27746.gif

source_name: Brain (cerebellum)

tag: Brain (cerebellum)


title: G5 temp retina

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27674.gif

source_name: G5 temp retina

tag: G5 temp retina


title: G5 macula

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27673.gif

source_name: G5 macula

tag: G5 macula


title: Dauer MTC#1T6 (red, channel 2) vs. RefB-JW (green, channel 1)

status: Public on Aug 20 2005

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11157.gif

data_processing: VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Caenorhabditis elegans

source_name: RefB-JW (green)

tag: RefB-JW (green)

source_name: Dauer MTC#1T6 (red)

tag: Dauer MTC#1T6 (red)


title: G5 cornea

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27672.gif

source_name: Stratagene Universal Human Reference 1 (Amp 7/12/01)

source_name: G5 cornea

tag: G5 cornea


title: Dauer MTC#1T10 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11158.gif

source_name: Dauer MTC#1T10 (red)

tag: Dauer MTC#1T10 (red)


title: G2 Optic Nerve

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20654.gif

tag: Stratagene Universal Human Reference 1 (Amp 7/12/01)

source_name: G2 Optic Nerve

tag: G2 Optic Nerve


title: Dauer MTC#2T10 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11152.gif

source_name: Dauer MTC#2T10 (red)

tag: Dauer MTC#2T10 (red)


title: Dauer MTC#1T12 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11159.gif

source_name: Dauer MTC#1T12 (red)

tag: Dauer MTC#1T12 (red)


title: Dauer MTC#4T4 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11153.gif

source_name: Dauer MTC#4T4 (red)

tag: Dauer MTC#4T4 (red)


title: L1 MTC#4T1 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13834.gif

source_name: L1 MTC#4T1 (red)

tag: L1 MTC#4T1 (red)


title: L1 MTC#4T0 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13833.gif

source_name: L1 MTC#4T0 (red)

tag: L1 MTC#4T0 (red)


title: Brain (frontal)

description:
Simple annotation: Normal tissue, Brain
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27745.gif

source_name: Brain (frontal)

tag: Brain (frontal)


title: Dauer MTC#4T12-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11513.gif

source_name: Dauer MTC#4T12-2 (red)

tag: Dauer MTC#4T12-2 (red)


title: L1 MTC#4T2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13837.gif

source_name: L1 MTC#4T2 (red)

tag: L1 MTC#4T2 (red)


title: L1 MTC#3T8 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13830.gif

source_name: L1 MTC#3T8 (red)

tag: L1 MTC#3T8 (red)


title: G1 Ciliary body

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18600.gif

source_name: G1 Ciliary body

tag: G1 Ciliary body


title: Dauer MTC#1T5 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11156.gif

source_name: Dauer MTC#1T5 (red)

tag: Dauer MTC#1T5 (red)


title: G1 Lens

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18601.gif

source_name: G1 Lens

tag: G1 Lens


title: G1 Retina

description:
Simple annotation: Normal tissue, Eye
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18597.gif

source_name: G1 Retina

tag: G1 Retina


title: Dauer MTC#2T0 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10813.gif

source_name: RefB-JW (green)

tag: RefB-JW (green)

source_name: Dauer MTC#2T0 (red)

tag: Dauer MTC#2T0 (red)


title: L1 MTC#1T3 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13796.gif

source_name: L1 MTC#1T3 (red)

tag: L1 MTC#1T3 (red)


title: L1 MTC#1T2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13795.gif

source_name: L1 MTC#1T2 (red)

tag: L1 MTC#1T2 (red)


title: Dauer MTC#1T1 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10492.gif

source_name: RefB-JW (green, channel 1)

tag: RefB-JW (green, channel 1)

source_name: Dauer Exit MTC #1, T1h (red, channel 2)

tag: Dauer Exit MTC #1, T1h (red, channel 2)


title: Dauer MTC#1T8 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs//10811.gif

source_name: Dauer MTC#1T8 (red)

tag: Dauer MTC#1T8 (red)


title: L1 MTC#1T5 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13798.gif

source_name: L1 MTC#1T5 (red)

tag: L1 MTC#1T5 (red)


title: L1 MTC#1T1 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13794.gif

source_name: L1 MTC#1T1 (red)

tag: L1 MTC#1T1 (red)


title: L1 MTC#1T4 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13797.gif

source_name: L1 MTC#1T4 (red)

tag: L1 MTC#1T4 (red)


title: L1 MTC#2T0 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13799.gif

source_name: L1 MTC#2T0 (red)

tag: L1 MTC#2T0 (red)


title: L1 MTC#3T1 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13821.gif

source_name: L1 MTC#3T1 (red)

tag: L1 MTC#3T1 (red)


title: L1 MTC#3T7 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13829.gif

source_name: L1 MTC#3T7 (red)

tag: L1 MTC#3T7 (red)


title: L1 MTC#3T4 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13824.gif

source_name: L1 MTC#3T4 (red)

tag: L1 MTC#3T4 (red)


title: L1 MTC#3T0 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13820.gif

source_name: L1 MTC#3T0 (red)

tag: L1 MTC#3T0 (red)


title: L1 MTC#3T3 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13823.gif

source_name: L1 MTC#3T3 (red)

tag: L1 MTC#3T3 (red)


title: Dauer MTC#4T1 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11177.gif

source_name: Dauer MTC#4T1 (red)

tag: Dauer MTC#4T1 (red)


title: Dauer MTC#3T7 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11174.gif

source_name: RefB-JW (green)

tag: RefB-JW (green)

source_name: Dauer MTC#3T7 (red)

tag: Dauer MTC#3T7 (red)


title: Dauer MTC#1T3 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10807.gif

source_name: Dauer MTC#1T3 (red)

tag: Dauer MTC#1T3 (red)


title: L1 MTC#1T0 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13793.gif

source_name: L1 MTC#1T0 (red)

tag: L1 MTC#1T0 (red)


title: Dauer MTC#3T10 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11175.gif

source_name: Dauer MTC#3T10 (red)

tag: Dauer MTC#3T10 (red)


title: Dauer MTC#3T12-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11176.gif

source_name: Dauer MTC#3T12-2 (red)

tag: Dauer MTC#3T12-2 (red)


title: Dauer MTC#1T4-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11495.gif

source_name: Dauer MTC#1T4-2 (red)

tag: Dauer MTC#1T4-2 (red)


title: L1 MTC#4T10 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13852.gif

source_name: L1 MTC#4T10 (red)

tag: L1 MTC#4T10 (red)


title: L1 MTC#2T8 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13816.gif

source_name: L1 MTC#2T8 (red)

tag: L1 MTC#2T8 (red)


title: L1 MTC#4T12 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13853.gif

source_name: L1 MTC#4T12 (red)

tag: L1 MTC#4T12 (red)


title: Dauer MTC#3T6 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11170.gif

source_name: Dauer MTC#3T6 (red)

tag: Dauer MTC#3T6 (red)


title: Dauer MTC#2T1 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11496.gif

source_name: Dauer MTC#2T1 (red)

tag: Dauer MTC#2T1 (red)


title: L1 MTC#4T8 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13851.gif

source_name: L1 MTC#4T8 (red)

tag: L1 MTC#4T8 (red)


title: Dauer MTC#2T2-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11497.gif

source_name: Dauer MTC#2T2-2 (red)

tag: Dauer MTC#2T2-2 (red)


title: Dauer MTC#1T2-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11494.gif

source_name: Dauer MTC#1T2-2 (red)

tag: Dauer MTC#1T2-2 (red)


title: L1 MTC#2T10 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13817.gif

source_name: L1 MTC#2T10 (red)

tag: L1 MTC#2T10 (red)


title: L1 MTC#3T2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13872.gif

source_name: L1 MTC#3T2 (red)

tag: L1 MTC#3T2 (red)


title: Dauer MTC#3T8 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10830.gif

source_name: RefB-JW (green)

tag: RefB-JW (green)

source_name: Dauer MTC#3T8 (red)

tag: Dauer MTC#3T8 (red)


title: L1 MTC#3T10 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13831.gif

source_name: L1 MTC#3T10 (red)

tag: L1 MTC#3T10 (red)


title: L1 MTC#3T12 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13832.gif

source_name: L1 MTC#3T12 (red)

tag: L1 MTC#3T12 (red)


title: Dauer MTC#3T4 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11168.gif

source_name: Dauer MTC#3T4 (red)

tag: Dauer MTC#3T4 (red)


title: Dauer MTC#3T2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11167.gif

source_name: Dauer MTC#3T2 (red)

tag: Dauer MTC#3T2 (red)


title: L1 MTC#2T7 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13815.gif

source_name: L1 MTC#2T7 (red)

tag: L1 MTC#2T7 (red)


title: L1 MTC#3T6 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13827.gif

source_name: L1 MTC#3T6 (red)

tag: L1 MTC#3T6 (red)


title: Dauer MTC#3T1 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11166.gif

source_name: Dauer MTC#3T1 (red)

tag: Dauer MTC#3T1 (red)


title: Dauer MTC#2T12 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11165.gif

source_name: Dauer MTC#2T12 (red)

tag: Dauer MTC#2T12 (red)


title: Dauer MTC#4T6-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11505.gif

source_name: Dauer MTC#4T6-2 (red)

tag: Dauer MTC#4T6-2 (red)


title: L1 MTC#2T12 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13818.gif

source_name: L1 MTC#2T12 (red)

tag: L1 MTC#2T12 (red)


title: Dauer MTC#2T7 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11164.gif

source_name: Dauer MTC#2T7 (red)

tag: Dauer MTC#2T7 (red)


title: Dauer MTC#2T6 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11163.gif

source_name: Dauer MTC#2T6 (red)

tag: Dauer MTC#2T6 (red)


title: Dauer MTC#4T10-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11511.gif

source_name: Dauer MTC#4T10-2 (red)

tag: Dauer MTC#4T10-2 (red)


title: Dauer MTC#3T5 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11169.gif

source_name: Dauer MTC#3T5 (red)

tag: Dauer MTC#3T5 (red)


title: L1 MTC#3T5 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13826.gif

source_name: L1 MTC#3T5 (red)

tag: L1 MTC#3T5 (red)


title: Dauer Adjust #3 T12 (red, channel 2) vs RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20290.gif

source_name: RefB-JW

tag: RefB-JW

source_name: Dauer Adjust #3 T12

tag: Dauer Adjust #3 T12


title: Dauer Adjust #3 T0 (red, channel 2) vs RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20287.gif

source_name: Dauer Adjust #3 T0

tag: Dauer Adjust #3 T0


title: Dauer MTC#4T5-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11504.gif

source_name: RefB-JW (green)

tag: RefB-JW (green)

source_name: Dauer MTC#4T5-2 (red)

tag: Dauer MTC#4T5-2 (red)


title: Dauer MTC#2T3-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11161.gif

source_name: Dauer MTC#2T3-2 (red)

tag: Dauer MTC#2T3-2 (red)


title: L1 MTC#4T6 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13849.gif

source_name: L1 MTC#4T6 (red)

tag: L1 MTC#4T6 (red)


title: Dauer MTC#2T5 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11162.gif

source_name: Dauer MTC#2T5 (red)

tag: Dauer MTC#2T5 (red)


title: Dauer MTC#4T0-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11501.gif

source_name: Dauer MTC#4T0-2 (red)

tag: Dauer MTC#4T0-2 (red)


title: L1 MTC#2T4 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13807.gif

source_name: L1 MTC#2T4 (red)

tag: L1 MTC#2T4 (red)


title: Dauer MTC#4T2-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11502.gif

source_name: Dauer MTC#4T2-2 (red)

tag: Dauer MTC#4T2-2 (red)


title: Dauer MTC#4T7 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs//11506.gif

source_name: Dauer MTC#4T7 (red)

tag: Dauer MTC#4T7 (red)


title: L1 MTC#1T10 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13806.gif

source_name: L1 MTC#1T10 (red)

tag: L1 MTC#1T10 (red)


title: Dauer MTC#3T3-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11500.gif

source_name: Dauer MTC#3T3-2 (red)

tag: Dauer MTC#3T3-2 (red)


title: L1 MTC#4T5 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13847.gif

source_name: L1 MTC#4T5 (red)

tag: L1 MTC#4T5 (red)


title: Dauer MTC#4T3-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11503.gif

source_name: Dauer MTC#4T3-2 (red)

tag: Dauer MTC#4T3-2 (red)


title: Dauer MTC#3T0-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11499.gif

source_name: Dauer MTC#3T0-2 (red)

tag: Dauer MTC#3T0-2 (red)


title: L1 MTC#1T12 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13809.gif

source_name: L1 MTC#1T12 (red)

tag: L1 MTC#1T12 (red)


title: Dauer Adjust #4 T12 (red, channel 2) vs RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20285.gif

source_name: RefB-JW

tag: RefB-JW

source_name: Dauer Adjust #4 T12

tag: Dauer Adjust #4 T12


title: L1 MTC#1T8 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13804.gif

source_name: RefB-JW (green)

tag: RefB-JW (green)

source_name: L1 MTC#1T8 (red)

tag: L1 MTC#1T8 (red)


title: L1 MTC#2T6 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13814.gif

source_name: L1 MTC#2T6 (red)

tag: L1 MTC#2T6 (red)


title: L1 MTC#2T3 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13805.gif

source_name: L1 MTC#2T3 (red)

tag: L1 MTC#2T3 (red)


title: Dauer Adjust #2 T12 (red, channel 2) vs RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20283.gif

source_name: Dauer Adjust #2 T12

tag: Dauer Adjust #2 T12


title: Dauer Adjust #4 T0 (red, channel 2) vs RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20284.gif

source_name: Dauer Adjust #4 T0

tag: Dauer Adjust #4 T0


title: L1 MTC#4T7 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13850.gif

source_name: L1 MTC#4T7 (red)

tag: L1 MTC#4T7 (red)


title: L1 MTC#1T7 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13802.gif

source_name: L1 MTC#1T7 (red)

tag: L1 MTC#1T7 (red)


title: L1 MTC#2T2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13803.gif

source_name: L1 MTC#2T2 (red)

tag: L1 MTC#2T2 (red)


title: L1 MTC#4T4 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13844.gif

source_name: L1 MTC#4T4 (red)

tag: L1 MTC#4T4 (red)


title: Dauer Adjust #1 T12 (red, channel 2) vs RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20279.gif

source_name: Dauer Adjust #1 T12

tag: Dauer Adjust #1 T12


title: Dauer Adjust #2 T0 (red, channel 2) vs RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20281.gif

source_name: Dauer Adjust #2 T0

tag: Dauer Adjust #2 T0


title: Dauer MTC#1T0-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11492.gif

source_name: Dauer MTC#1T0-2 (red)

tag: Dauer MTC#1T0-2 (red)


title: L1 MTC#4T3 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13841.gif

source_name: L1 MTC#4T3 (red)

tag: L1 MTC#4T3 (red)


title: G27 genomic DNA vs. TIGR/Astra reference.

status: Public on Aug 16 2005

type: genomic

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-11/1316.gif

molecule: genomic DNA

organism: Helicobacter pylori

source_name: 1ug tigr genomic DNA, 1ug Astra genomic DNA

source_name: 2ug G27 genomic DNA (wizard prep)

tag: 2ug G27 genomic DNA (wizard prep)


title: J99-C6-3 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18850.gif

source_name: 250 ng Tigr/Astra genomic DNA

tag: 250 ng Tigr/Astra genomic DNA

source_name: 250 ng J99-C6 genomic DNA

tag: 250 ng J99-C6 genomic DNA


title: J99-C6-5 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17832.gif


title: Sydney strian genomic DNA vs astra/tigr ref.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-11/1029.gif

source_name: 1ug TIGR genomic DNA, 1ug Astra genomic DNA

source_name: 2 ug Sydney Genomic DNA (wizard prep)

tag: 2 ug Sydney Genomic DNA (wizard prep)


title: Dauer MTC#4T8 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10828.gif

source_name: RefB-JW (green)

tag: RefB-JW (green)

source_name: Dauer MTC#4T8 (red)

tag: Dauer MTC#4T8 (red)


title: J99-4 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17830.gif

source_name: 250 ng J99 genomic DNA

tag: 250 ng J99 genomic DNA


title: Dauer Adjust #1 T0 (red, channel 2) vs RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20276.gif

source_name: RefB-JW

tag: RefB-JW

source_name: Dauer Adjust #1 T0

tag: Dauer Adjust #1 T0


title: 292 genomic DNA vs TIGR/ASTRA reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-11/1315.gif

source_name: 1ug TIGR genomic DNA, 1ug Astra Genomic DNA

source_name: 2 ug 292genomic DNA, wizard prep

tag: 2 ug 292genomic DNA, wizard prep


title: L1 MTC#1T6 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13800.gif

source_name: L1 MTC#1T6 (red)

tag: L1 MTC#1T6 (red)


title: J99-C10-3 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17833.gif

source_name: 250 ng J99-C10 genomic DNA

tag: 250 ng J99-C10 genomic DNA


title: Sydney wizard prep genomic DNA vs TIGR/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-11/1317.gif

source_name: 1 ug tigr genomic DNA, 1ug Asgra genomic DNA

source_name: 2 ug sydney strain genomic DNA, wizard prep


title: G27 genomic DNA vs astra/tigr ref.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-11/1028.gif

tag: 1ug TIGR genomic DNA, 1ug Astra genomic DNA

source_name: 2 ug G27 Genomic DNA (wizard prep)

tag: 2 ug G27 Genomic DNA (wizard prep)


title: L1 MTC#2T1 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13801.gif

source_name: L1 MTC#2T1 (red)

tag: L1 MTC#2T1 (red)


title: L1 MTC#2T5 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13811.gif

source_name: L1 MTC#2T5 (red)

tag: L1 MTC#2T5 (red)


title: 292 genomic DNA vs astra/tigr ref.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-11/1027.gif

source_name: 2 ug 292 Genomic DNA (wizard prep)

tag: 2 ug 292 Genomic DNA (wizard prep)


title: 326 genomic DNA vs. Tigr/Astra reference III.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1457.gif

source_name: 1ug Tigr genomic DNA, 1ug Astra genomic DNA

source_name: 2 ug 326 genomic DNA

tag: 2 ug 326 genomic DNA


title: G39 genomic DNA vs. Tigr/Astra reference DNA III.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1456.gif

source_name: 1ug Tigr genomic DNA, 1 ug Astra genomic DNA

source_name: 2 ug G39 genomic DNA

tag: 2 ug G39 genomic DNA


title: J99-D3-3 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18849.gif

source_name: 250 ng Tigr/Astra genomic DNA

tag: 250 ng Tigr/Astra genomic DNA

source_name: 250 ng J99-D3 genomic DNA

tag: 250 ng J99-D3 genomic DNA


title: Dauer MTC#2T8-2 (red, channel 2) vs. RefB-JW (green, channel 1)

description:
Simple annotation: dauer, development
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11498.gif

source_name: RefB-JW (green)

tag: RefB-JW (green)

source_name: Dauer MTC#2T8-2 (red)

tag: Dauer MTC#2T8-2 (red)


title: J99-Cardia-3 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18848.gif

source_name: 250 ng J99-Cardia genomic DNA

tag: 250 ng J99-Cardia genomic DNA


title: perR_vs_wt_A_Cy5-perR

description:
Simple annotation: Strain comparison, Knock-out
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25863.gif

organism: Bacillus subtilis

source_name: experimental sample

tag: experimental sample


title: G50 genomic DNA vs. Tigr/Astra reference III.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1455.gif

source_name: 1 ug Tigr genomic DNA, 1 ug Astra genomic DNA

source_name: 2 ug G50 genomic DNA

tag: 2 ug G50 genomic DNA


title: CCUG genomic DNA vs. Tigr/Astra reference III.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1454.gif

tag: 1ug Tigr genomic DNA, 1ug Astra genomic DNA

source_name: 2 ug CCUG genomic DNA

tag: 2 ug CCUG genomic DNA


title: perR_vs_wt_B_Cy5-perR

description:
Simple annotation: Strain comparison, Knock-out
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25864.gif


title: perR_vs_wt_F_Cy5-wt

description:
Simple annotation: Strain comparison, Knock-out
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25868.gif


title: J99-A9-3 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18847.gif

source_name: 250 ng J99-A9 genomic DNA

tag: 250 ng J99-A9 genomic DNA


title: perR_vs_wt_C_Cy5-perR

description:
Simple annotation: Strain comparison, Knock-out
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25865.gif


title: tert-butyl_peroxide_100uM_t0A

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22947.gif


title: J99-A3-3 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18844.gif

source_name: 250 ng J99-A3 genomic DNA

tag: 250 ng J99-A3 genomic DNA


title: 87A genomic DNA vs. Tigr/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1450.gif

tag: 1 ug Tigr genomic DNA, 1 ug Astra genomic DNA

source_name: 2 ug 87A genomic DNA

tag: 2 ug 87A genomic DNA


title: G39 genomic DNA vs. Tigr/Astra reference DNA.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1452.gif


title: tert-butyl_alcohol_100uM_t3C

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22948.gif


title: J99-A1-3vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18843.gif

source_name: 250 ng J99-A1 genomic DNA

tag: 250 ng J99-A1 genomic DNA


title: J99-A7-5 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18846.gif

source_name: 250 ng J99-A7 genomic DNA

tag: 250 ng J99-A7 genomic DNA


title: Heat_37C_t0A_Bs051

description:
Simple annotation: Heat shock, Heat steady
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22588.gif


title: J99-A5-3 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18845.gif

source_name: 250 ng J99-A5 genomic DNA

tag: 250 ng J99-A5 genomic DNA


title: tert-butyl_peroxide_100uM_t10C

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22944.gif


title: tert-butyl_peroxide_100uM_t10A

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22946.gif


title: perR_vs_wt_E_Cy5-wt

description:
Simple annotation: Strain comparison, Knock-out
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25867.gif


title: Heat_37C_t10A_Bs053

description:
Simple annotation: Heat shock, Heat steady
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22589.gif


title: tert-butyl_peroxide_100uM_t10B

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22945.gif


title: perR_vs_wt_D_Cy5-wt

description:
Simple annotation: Strain comparison, Knock-out
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25866.gif


title: tert-butyl_peroxide_100uM_t20A

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22942.gif


title: J99-D1-1 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17828.gif

source_name: 250 ng J99-D1 genomic DNA

tag: 250 ng J99-D1 genomic DNA


title: J99-A3-1 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18199.gif

tag: 250 ng Tigr/Astra genomic DNA


title: J99-C3-2 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17826.gif

source_name: 250 ng J99-C3 genomic DNA

tag: 250 ng J99-C3 genomic DNA


title: J99-3 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17827.gif

source_name: 250 ng Tigr/Astra genomic DNA

source_name: 250 ng J99 genomic DNA

tag: 250 ng J99 genomic DNA


title: J99-D1-2 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17829.gif


title: J99-C3-1 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17825.gif


title: peroxide_58uM_t20A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22369.gif


title: peroxide_58uM_t10C

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22368.gif


title: J99-D3-1 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18197.gif

source_name: 250 ng J99-D3 genomic DNA

tag: 250 ng J99-D3 genomic DNA


title: peroxide_58uM_t10B

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22367.gif


title: 342S genomic DNA vs. Tigr/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1446.gif

source_name: 1ug Tigr genomic DNA, 1ug Astra genomic DNA

source_name: 2 ug 342S genomic DNA

tag: 2 ug 342S genomic DNA


title: J99-A5-2 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17824.gif


title: J99-D3-2 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18198.gif


title: tert-butyl_peroxide_100uM_t20B

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22940.gif

source_name: experimental sample

tag: experimental sample


title: peroxide_58uM_t0A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22365.gif


title: peroxide_8uM_t20C

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22361.gif


title: tert-butyl_peroxide_100uM_t3B

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22938.gif


title: tert-butyl_peroxide_100uM_t3A

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22939.gif


title: CCUG genomic DNA vs. Tigr/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1447.gif

source_name: 1ug Tigr genomic DNA, 1 ug Astra genomic DNA


title: peroxide_58uM_t10A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22366.gif


title: 314 genomic DNA vs. Tigr/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1444.gif

tag: 1ug Tigr genomic DNA, 1 ug Astra genomic DNA

source_name: 2 ug 314 genomic DNA

tag: 2 ug 314 genomic DNA


title: J99-Cardia 1-1 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17821.gif

source_name: 250 ng J99-Cardia 1 genomic DNA

tag: 250 ng J99-Cardia 1 genomic DNA


title: tert-butyl_peroxide_100uM_t3C

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22937.gif


title: peroxide_8uM_t3A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22362.gif


title: G39 genomic DNA vs. Tigr/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1440.gif

source_name: 2 ug G39 genomic DNA

tag: 2 ug G39 genomic DNA


title: peroxide_8uM_t3C

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22364.gif


title: peroxide_8uM_t3B

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22363.gif


title: peroxide_8uM_t20B

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22360.gif


title: Hp1 genomic DNA vs. Tigr/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1445.gif

source_name: 1 ug Tigr genomic DNA, 1 ug Astra genomic DNA

source_name: 2 ug Hp1 genomic DNA

tag: 2 ug Hp1 genomic DNA


title: G50 genomic DNA vs. Tigr/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1443.gif

tag: 1 ug Tigr genomic DNA, 1 ug Astra genomic DNA

source_name: 2 ug G50 genomic DNA

tag: 2 ug G50 genomic DNA


title: J99-Cardia 1-2 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17822.gif


title: 87A genomic DNA vs Tigr/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-01/1767.gif

tag: 1ug Tigr genomic DNA, 1ug Astra genomic DNA

source_name: 2ug 87A genomic DNA

tag: 2ug 87A genomic DNA


title: 292 genomic DNA vs Tigr/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-01/1766.gif

source_name: 2ug 292 genomic DNA

tag: 2ug 292 genomic DNA


title: 326 genomic DNA vs Tigr/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-01/1765.gif

source_name: 2ug 326 genomic DNA

tag: 2ug 326 genomic DNA


title: 314 vs. Tigr/Astra ref trial 3.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5362.gif

source_name: 0.7 ug Astra genomic DNA +0.7 ug Tigr genomic DNA

source_name: 2ug 314 genomic DNA

tag: 2ug 314 genomic DNA


title: Heat_48C_t3B_Bs062

description:
Simple annotation: Heat shock, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22604.gif


title: CCUG genomic DNA vs Tigr/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1439.gif

source_name: 2ug CCUG genomic DNA

tag: 2ug CCUG genomic DNA


title: Heat_48C_t3A_Bs059

description:
Simple annotation: Heat shock, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22602.gif


title: peroxide_0uM_t40C

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22354.gif


title: peroxide_0uM_t40A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22352.gif


title: peroxide_0uM_t3B

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22350.gif


title: J99-A1-3 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18213.gif

source_name: 250 ng Tigr/Astra genomic DNA

tag: 250 ng Tigr/Astra genomic DNA

source_name: 250 ng J99-A1 genomic DNA

tag: 250 ng J99-A1 genomic DNA


title: peroxide_8uM_t10A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22356.gif


title: peroxide_8uM_t10C

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22358.gif


title: peroxide_8uM_t10B

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22357.gif


title: j99-c10 250 ng trial 1.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16576.gif

source_name: 250 ng Tigr/Astra Reference

tag: 250 ng Tigr/Astra Reference


title: J99-A7-4 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18212.gif

source_name: 250 ng J99-A7 genomic DNA

tag: 250 ng J99-A7 genomic DNA


title: peroxide_0uM_t40B

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22353.gif

source_name: experimental sample

tag: experimental sample


title: J99-A7-3 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18211.gif


title: j99-c6 250 ng trial 1.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16572.gif


title: J99-A3-2 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18209.gif

source_name: 250 ng J99-A3 genomic DNA

tag: 250 ng J99-A3 genomic DNA


title: j99-c12 250 ng trial 1.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16577.gif


title: peroxide_8uM_t0A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22355.gif


title: J99-A1-2 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18208.gif


title: j99-c12 250 ng trial 2.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16578.gif


title: j99-c6 250 ng trial 2.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16574.gif


title: peroxide_0uM_t3C

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22351.gif


title: G50 genomic DNA vs Tigr/Astra reference.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/1438.gif

source_name: 1ug Tigr genomic DNA, 1ug Astra genomic DNA

source_name: 2ug G50 genomic DNA

tag: 2ug G50 genomic DNA


title: Heat_48C_t20A_Bs061

description:
Simple annotation: Heat shock, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22600.gif


title: tert-butyl_alcohol_100uM_t0A

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22963.gif


title: j99 vs tigr/astra reference (0.25 ug) 2.

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17119.gif

source_name: 0.25 ug tigr/astra reference

tag: 0.25 ug tigr/astra reference

source_name: 0.25 ug j99 genomic DNA

tag: 0.25 ug j99 genomic DNA


title: J99-A9-1 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18205.gif

source_name: 250 ng J99-A9 genomic DNA

tag: 250 ng J99-A9 genomic DNA


title: peroxide_0uM_t20A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22346.gif


title: Heat_48C_t20B_Bs064

description:
Simple annotation: Heat shock, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22601.gif


title: J99-A1-1 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18207.gif


title: peroxide_0uM_t3A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22349.gif


title: peroxide_0uM_t20B

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22347.gif


title: tert-butyl_alcohol_100uM_t10B

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22960.gif


title: J99-A9-2 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18206.gif


title: J99-C6-1 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18203.gif

source_name: 250 ng J99-C6 genomic DNA

tag: 250 ng J99-C6 genomic DNA


title: peroxide_0uM_t20C

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22348.gif


title: j99 vs tigr/astra reference (0.25 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17118.gif


title: peroxide_0uM_t10A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22343.gif


title: J99-A5-1 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17823.gif

source_name: 250 ng J99-A5 genomic DNA

tag: 250 ng J99-A5 genomic DNA


title: peroxide_8uM_t20A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22359.gif


title: tert-butyl_alcohol_100uM_t10A

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22961.gif


title: J99-C6-2 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18204.gif


title: J99-C3-3 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18852.gif

source_name: 250 ng J99-C3 genomic DNA

tag: 250 ng J99-C3 genomic DNA


title: peroxide_0uM_t10C

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22345.gif


title: peroxide_0uM_t0B

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22342.gif


title: peroxide_0uM_t10B

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22344.gif


title: J99-A7-2 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18201.gif


title: J99-C6-4 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18851.gif


title: J99-A7-1 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18200.gif


title: tert-butyl_alcohol_100uM_t3B

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22950.gif


title: J99-D1-3 vs Tigr/Astra references (250 ug).

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18853.gif

source_name: 250 ng J99-D1 genomic DNA

tag: 250 ng J99-D1 genomic DNA


title: peroxide_0uM_t0A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22341.gif


title: Heat_48C_t10B_Bs063

description:
Simple annotation: Heat shock, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22599.gif


title: tert-butyl_alcohol_100uM_t20B

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22954.gif


title: Heat_37C_t3B_Bs066

description:
Simple annotation: Heat shock, Heat steady
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22596.gif


title: tert-butyl_alcohol_100uM_t3A

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22951.gif


title: Heat_37C_t3B_Bs055

description:
Simple annotation: Heat shock, Heat steady
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22594.gif


title: Heat_37C_t20A_Bs054

description:
Simple annotation: Heat shock, Heat steady
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22591.gif


title: Heat_48C_t10A_Bs060

description:
Simple annotation: Heat shock, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22598.gif


title: tert-butyl_alcohol_100uM_t20A

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22956.gif


title: Heat_37C_t20B_Bs057

description:
Simple annotation: Heat shock, Heat steady
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22592.gif


title: tert-butyl_alcohol_100uM_t10C

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22958.gif


title: peroxide_58uM_t40A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22375.gif


title: Heat_37C_t3A_Bs052

description:
Simple annotation: Heat shock, Heat steady
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22593.gif


title: peroxide_58uM_t3C

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22374.gif


title: tert-butyl_alcohol_100uM_t20C

description:
Simple annotation: Chemical effects, oxidation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22953.gif


title: Tunicamycin vs. Ctrl

description:
Simple annotation: Unfolded Protein Response, tunicamycin
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/298.gif

organism: Saccharomyces cerevisiae

source_name: Ctrl

tag: Ctrl

source_name: Tunicamycin

tag: Tunicamycin


title: peroxide_58uM_t40B

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22376.gif


title: peroxide_58uM_t3B

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22373.gif


title: Heat_37C_t0B_Bs065

description:
Simple annotation: Heat shock, Heat steady
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22595.gif


title: Heat_37C_t10B_Bs056

description:
Simple annotation: Heat shock, Heat steady
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22590.gif


title: SWIIIB3A

status: Public on Aug 13 2005

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15990.gif

organism: Toxoplasma gondii

source_name: Ref

tag: Ref


title: Heat_48C_t0A_Bs058

description:
Simple annotation: Heat shock, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22597.gif


title: peroxide_58uM_t20C

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22371.gif


title: SWIIIB4B

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17585.gif

source_name: T3 - T7 ref

tag: T3 - T7 ref

source_name: day 4 brady

tag: day 4 brady


title: SWIIIB3B

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17584.gif

source_name: day 3 brady

tag: day 3 brady


title: SWIIIB2B

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/17931.gif

source_name: ref

tag: ref

source_name: SWIII B2

tag: SWIII B2


title: peroxide_58uM_t3A

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22372.gif

source_name: experimental sample

tag: experimental sample


title: SWIVT2B

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/17867.gif

source_name: SWIVc T2

tag: SWIVc T2


title: SWIVT2A

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16531.gif

source_name: T3-T7 Ref

tag: T3-T7 Ref


title: Kb vs. Ctrl

description:
Simple annotation: Unfolded Protein Response, MHC
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/297.gif

source_name: Kb

tag: Kb


title: peroxide_58uM_t40C

description:
Simple annotation: Chemical effects, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22377.gif


title: SWIIIT2B

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17582.gif

source_name: T3 - T7 Ref

tag: T3 - T7 Ref

source_name: day 2 tachy

tag: day 2 tachy


title: SWIVB4B

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/17872.gif

source_name: SWIV B4

tag: SWIV B4


title: SWIVB2A

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16532.gif

source_name: T3-T7 Ref (5/7/01) prep + MC ESTs

tag: T3-T7 Ref (5/7/01) prep + MC ESTs

source_name: B2 RNA

tag: B2 RNA


title: SWIVB4A

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16534.gif

source_name: B4 RNA

tag: B4 RNA


title: SWIIIT2A

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15987.gif


title: Mariana's mutant B7 4 day in-vitro switch brady (red ink) vs. T3/T7 ref.

description:
Simple annotation: Toxoplasma, Differentiation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17166.gif

source_name: Parasites

tag: Parasites


title: SWIIIB2A

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15989.gif

source_name: Ref

tag: Ref


title: SWIVB2B

description:
Simple annotation: bradyzoite, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/17868.gif

source_name: SWIVc B2

tag: SWIVc B2