title: New N2 mixed stage (red, channel 2) vs.L2 N2  T2new.4 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11092.gif

source_name: L2 N2  T2new.4 (green, channel 1)

tag: L2 N2  T2new.4 (green, channel 1)


title: New N2 mixed stage (red, channel 2) vs.L2 N2  T30.2 (green, channel 1)

status: Public on Jul 22 2005

type: RNA

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11077.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)

molecule: total RNA

organism: Caenorhabditis elegans

source_name: L2 N2  T30.2 (green, channel 1)

tag: L2 N2  T30.2 (green, channel 1)

source_name: New N2 mixed stage (red, channel 2)

tag: New N2 mixed stage (red, channel 2)


title: New N2 mixed stage (red, channel 2) vs.L2 N2  T0.2 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11076.gif

source_name: L2 N2  T0.2 (green, channel 1)

tag: L2 N2  T0.2 (green, channel 1)


title: New N2 mixed stage (red, channel 2) vs.L2 Ras  T0.1 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs//11110.gif

source_name: L2 Ras  T0.1 (green, channel 1)

tag: L2 Ras  T0.1 (green, channel 1)


title: New N2 mixed stage (red, channel 2) vs.L2 N2  T30.3 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11081.gif

source_name: L2 N2  T30.3 (green, channel 1)

tag: L2 N2  T30.3 (green, channel 1)


title: New N2 mixed stage (red, channel 2) vs.L2 N2  T1.1 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11075.gif

source_name: L2 N2  T1.1 (green, channel 1)

tag: L2 N2  T1.1 (green, channel 1)


title: New N2 mixed stage (red, channel 2) vs.L2 N2  T30.1 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11074.gif

source_name: L2 N2  T30.1 (green, channel 1)

tag: L2 N2  T30.1 (green, channel 1)


title: New N2 mixed stage (red, channel 2) vs.L2 N2  T0.4 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11138.gif

source_name: L2 N2  T0.4 (green, channel 1)

tag: L2 N2  T0.4 (green, channel 1)


title: New N2 mixed stage (red, channel 2) vs.L2 N2  T0.1 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11073.gif

source_name: L2 N2  T0.1 (green, channel 1)

tag: L2 N2  T0.1 (green, channel 1)


title: New N2 mixed stage (red, channel 2) vs.L2 N2  T2new.3 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11090.gif

source_name: L2 N2  T2new.3 (green, channel 1)

tag: L2 N2  T2new.3 (green, channel 1)


title: New N2 mixed stage (red, channel 2) vs.L2 Ras  T30.2 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11146.gif

source_name: L2 Ras  T30.2 (green, channel 1)

tag: L2 Ras  T30.2 (green, channel 1)


title: New N2 mixed stage (red, channel 2) vs.L2 Ras  T2.3 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs//11322.gif

source_name: L2 Ras  T2.3 (green, channel 1)

tag: L2 Ras  T2.3 (green, channel 1)

source_name: New N2 mixed stage (red, channel 2) vs.EGGS N2  T0.1 (green, channel 1)


title: New N2 mixed stage (red, channel 2) vs.L2 Ras  T0new.1 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs//11324.gif

source_name: L2 Ras  T0new.1 (green, channel 1)

tag: L2 Ras  T0new.1 (green, channel 1)


title: 6 hr Ameba Alone  5 4 03

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40330.gif

organism: Entamoeba histolytica

source_name: pHos PCR reference M13F M13R (1x)

tag: pHos PCR reference M13F M13R (1x)

source_name: 8ug 6hr ameba + alone RNA

tag: 8ug 6hr ameba + alone RNA


title: 9hr Ameba alone  (4/16 #2)

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40588.gif

source_name: pHos PCR reference M13F M13R (1x-350ng)

tag: pHos PCR reference M13F M13R (1x-350ng)

source_name: 8ug 6hr Ameba + Caco RNA

tag: 8ug 6hr Ameba + Caco RNA


title: New N2 mixed stage (red, channel 2) vs.L2 Ras  T30.4 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11120.gif

source_name: L2 Ras  T30.4 (green, channel 1)

tag: L2 Ras  T30.4 (green, channel 1)

source_name: New N2 mixed stage (red, channel 2)


title: New N2 mixed stage (red, channel 2) vs.L2 N2  T0new.1 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11140.gif

source_name: L2 N2  T0new.1 (green, channel 1)

tag: L2 N2  T0new.1 (green, channel 1)

tag: New N2 mixed stage (red, channel 2)


title: C18-1

description:
We developed a method called messenger RNA tagging to isolate muscle mRNA, because this tissue is difficult to isolate in C. elegans. The basis of the technique is to use a characterized promoter to express an epitope-tagged mRNA-binding protein, such as poly(A)-binding protein (PAB-1), in cells or tissues of interest. Because poly(A)-binding proteins bind tightly to the poly(A) tail of mRNAs, mRNAs from specific tissues can be enriched by cross-linking them to the tagged PAB-1, and co-immunoprecipitating the complex of mRNA and tagged PAB-1 using an anti-epitope monoclonal antibody. DNA microarrays can then be used to identify which mRNAs have been enriched by co-immunoprecipitation, indicating that the corresponding gene is expressed in the same cells as the tagged PAB-1.
To isolate the mRNA expressed in muscle, we first generated animals that express Flag::PAB-1 in non-pharyngeal muscles from an integrated transgene using the myo-3 promoter5. The mRNA-Flag::PAB-1 complex was co-immunoprecipitated from cell lysate using anti-Flag monoclonal antibodies.
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11539.gif

source_name: Pre-IP

tag: Pre-IP

source_name: Post-IP

tag: Post-IP


title: C18-6

description:
We developed a method called messenger RNA tagging to isolate muscle mRNA, because this tissue is difficult to isolate in C. elegans. The basis of the technique is to use a characterized promoter to express an epitope-tagged mRNA-binding protein, such as poly(A)-binding protein (PAB-1), in cells or tissues of interest. Because poly(A)-binding proteins bind tightly to the poly(A) tail of mRNAs, mRNAs from specific tissues can be enriched by cross-linking them to the tagged PAB-1, and co-immunoprecipitating the complex of mRNA and tagged PAB-1 using an anti-epitope monoclonal antibody. DNA microarrays can then be used to identify which mRNAs have been enriched by co-immunoprecipitation, indicating that the corresponding gene is expressed in the same cells as the tagged PAB-1.
To isolate the mRNA expressed in muscle, we first generated animals that express Flag::PAB-1 in non-pharyngeal muscles from an integrated transgene using the myo-3 promoter5. The mRNA-Flag::PAB-1 complex was co-immunoprecipitated from cell lysate using anti-Flag monoclonal antibodies.
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11545.gif


title: C18-5

description:
We developed a method called messenger RNA tagging to isolate muscle mRNA, because this tissue is difficult to isolate in C. elegans. The basis of the technique is to use a characterized promoter to express an epitope-tagged mRNA-binding protein, such as poly(A)-binding protein (PAB-1), in cells or tissues of interest. Because poly(A)-binding proteins bind tightly to the poly(A) tail of mRNAs, mRNAs from specific tissues can be enriched by cross-linking them to the tagged PAB-1, and co-immunoprecipitating the complex of mRNA and tagged PAB-1 using an anti-epitope monoclonal antibody. DNA microarrays can then be used to identify which mRNAs have been enriched by co-immunoprecipitation, indicating that the corresponding gene is expressed in the same cells as the tagged PAB-1.
To isolate the mRNA expressed in muscle, we first generated animals that express Flag::PAB-1 in non-pharyngeal muscles from an integrated transgene using the myo-3 promoter5. The mRNA-Flag::PAB-1 complex was co-immunoprecipitated from cell lysate using anti-Flag monoclonal antibodies.
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11544.gif


title: 6hr Ameba alone (4/16 #2)

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40586.gif

source_name: 8ug 6hr Ameba alone RNA

tag: 8ug 6hr Ameba alone RNA


title: 6hr ameba alone (2/2) flagged spots

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40593.gif

source_name: pHos PCR reference M13F M13 R (350ng)

tag: pHos PCR reference M13F M13 R (350ng)

source_name: 8 ug amebic RNA

tag: 8 ug amebic RNA


title: 6 hr Ameba + caco 5 4 03

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40331.gif

source_name: 8ug 6hr ameba + caco  RNA

tag: 8ug 6hr ameba + caco  RNA


title: 9 hr ameba + caco 5 4 03

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40334.gif

source_name: 8ug 9hr ameba + caco RNA

tag: 8ug 9hr ameba + caco RNA


title: C18-4

description:
We developed a method called messenger RNA tagging to isolate muscle mRNA, because this tissue is difficult to isolate in C. elegans. The basis of the technique is to use a characterized promoter to express an epitope-tagged mRNA-binding protein, such as poly(A)-binding protein (PAB-1), in cells or tissues of interest. Because poly(A)-binding proteins bind tightly to the poly(A) tail of mRNAs, mRNAs from specific tissues can be enriched by cross-linking them to the tagged PAB-1, and co-immunoprecipitating the complex of mRNA and tagged PAB-1 using an anti-epitope monoclonal antibody. DNA microarrays can then be used to identify which mRNAs have been enriched by co-immunoprecipitation, indicating that the corresponding gene is expressed in the same cells as the tagged PAB-1.
To isolate the mRNA expressed in muscle, we first generated animals that express Flag::PAB-1 in non-pharyngeal muscles from an integrated transgene using the myo-3 promoter5. The mRNA-Flag::PAB-1 complex was co-immunoprecipitated from cell lysate using anti-Flag monoclonal antibodies.
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11543.gif


title: 6hr Ameba + Caco (4/16 #2)

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40587.gif


title: 6hr Ameba + Caco (2/2)

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40579.gif

source_name: 11.5ug 6hr Amebic + Caco RNA

tag: 11.5ug 6hr Amebic + Caco RNA


title: New N2 mixed stage (red, channel 2) vs.L2 N2  T2new.1 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11142.gif

source_name: L2 N2  T2new.1 (green, channel 1)

tag: L2 N2  T2new.1 (green, channel 1)


title: 9hr Ameba + Caco  (4/16 #2)

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40589.gif

source_name: 8ug 9hr Ameba + Caco RNA

tag: 8ug 9hr Ameba + Caco RNA


title: New N2 mixed stage (red, channel 2) vs.L2 Ras  T1.4 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11121.gif

source_name: L2 Ras  T1.4 (green, channel 1)

tag: L2 Ras  T1.4 (green, channel 1)


title: New N2 mixed stage (red, channel 2) vs.L2 N2  T0new.4 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11091.gif

source_name: L2 N2  T0new.4 (green, channel 1)

tag: L2 N2  T0new.4 (green, channel 1)


title: 3hr Ameba alone (4/16 #2)

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40584.gif

source_name: pHos PCR reference M13F M13R (1x-350ng)

tag: pHos PCR reference M13F M13R (1x-350ng)

source_name: 8ug 3hr Ameba alone RNA

tag: 8ug 3hr Ameba alone RNA


title: 3hr Ameba + Caco (2/2) #2

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40583.gif

source_name: 13.5 3hr Ameba + Caco  RNA

tag: 13.5 3hr Ameba + Caco  RNA


title: C18-2

description:
We developed a method called messenger RNA tagging to isolate muscle mRNA, because this tissue is difficult to isolate in C. elegans. The basis of the technique is to use a characterized promoter to express an epitope-tagged mRNA-binding protein, such as poly(A)-binding protein (PAB-1), in cells or tissues of interest. Because poly(A)-binding proteins bind tightly to the poly(A) tail of mRNAs, mRNAs from specific tissues can be enriched by cross-linking them to the tagged PAB-1, and co-immunoprecipitating the complex of mRNA and tagged PAB-1 using an anti-epitope monoclonal antibody. DNA microarrays can then be used to identify which mRNAs have been enriched by co-immunoprecipitation, indicating that the corresponding gene is expressed in the same cells as the tagged PAB-1.
To isolate the mRNA expressed in muscle, we first generated animals that express Flag::PAB-1 in non-pharyngeal muscles from an integrated transgene using the myo-3 promoter5. The mRNA-Flag::PAB-1 complex was co-immunoprecipitated from cell lysate using anti-Flag monoclonal antibodies.
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11541.gif


title: 3hr Ameba alone (2/2)

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40576.gif

source_name: 8ug Amebic RNA alone

tag: 8ug Amebic RNA alone


title: 3hr Ameba + Cacp (4/16 #2)

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40585.gif

source_name: 12ug 3hr Ameba + Caco RNA

tag: 12ug 3hr Ameba + Caco RNA


title: 3hr Ameba + Caco (2/2)

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40577.gif

source_name: 13.5ug Amebic + Caco RNA

tag: 13.5ug Amebic + Caco RNA


title: 9hr Ameba + Caco (2/2)

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40581.gif

source_name: 11.3ug 9hr Ameba + Caco RNA

tag: 11.3ug 9hr Ameba + Caco RNA


title: DBY7286 + 0.3 mM H2O2 (20 min) b

description:
Simple annotation: Stress, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/691.gif

organism: Saccharomyces cerevisiae

source_name: time = 0 min

tag: time = 0 min

source_name: time = 20 min

tag: time = 20 min


title: New N2 mixed stage (red, channel 2) vs.L2 N2  T0new.2 (green, channel 1)

description:
Simple annotation: C. elegans, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11144.gif

source_name: L2 N2  T0new.2 (green, channel 1)

tag: L2 N2  T0new.2 (green, channel 1)

source_name: New N2 mixed stage (red, channel 2)

tag: New N2 mixed stage (red, channel 2)


title: EHE 007 No Heat Shock

description:
Simple annotation: control, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39129.gif

source_name: Reference pHOS PCR M13F M13R

tag: Reference pHOS PCR M13F M13R

source_name: 6 ug non-heat treated RNA

tag: 6 ug non-heat treated RNA


title: EHE 010  Heat Shock

description:
Simple annotation: control, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39131.gif

source_name: 6 ug heat treated RNA

tag: 6 ug heat treated RNA


title: EHE 011  Heat Shock

description:
Simple annotation: control, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39132.gif


title: 3 hr ameba alone 5 5 03

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40380.gif

source_name: pHos PCR reference M13F M13R (1x)

tag: pHos PCR reference M13F M13R (1x)

source_name: 8ug 3hr Amebic RNA

tag: 8ug 3hr Amebic RNA


title: 3hr Ameba alone (2/2) #2

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40582.gif

source_name: 8ug 3hr Ameba alone  RNA

tag: 8ug 3hr Ameba alone  RNA


title: 9hr ameba alone  5 5 03

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40383.gif

source_name: 8ug 9hr Amebic RNA

tag: 8ug 9hr Amebic RNA


title: 9hr Ameba alone (2/2)

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40580.gif

source_name: pHos PCR reference M13F M13R (1x-350ng)

tag: pHos PCR reference M13F M13R (1x-350ng)

source_name: 8ug 9hr Amebic  RNA

tag: 8ug 9hr Amebic  RNA


title: yap59 b

description:
Simple annotation: Transcription, Cell-cycle factors
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/8908.gif

source_name: wt

tag: wt

source_name: YAP1 overexpression

tag: YAP1 overexpression


title: EHE 008 No Heat Shock

description:
Simple annotation: control, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39130.gif


title: C18-3

description:
We developed a method called messenger RNA tagging to isolate muscle mRNA, because this tissue is difficult to isolate in C. elegans. The basis of the technique is to use a characterized promoter to express an epitope-tagged mRNA-binding protein, such as poly(A)-binding protein (PAB-1), in cells or tissues of interest. Because poly(A)-binding proteins bind tightly to the poly(A) tail of mRNAs, mRNAs from specific tissues can be enriched by cross-linking them to the tagged PAB-1, and co-immunoprecipitating the complex of mRNA and tagged PAB-1 using an anti-epitope monoclonal antibody. DNA microarrays can then be used to identify which mRNAs have been enriched by co-immunoprecipitation, indicating that the corresponding gene is expressed in the same cells as the tagged PAB-1.
To isolate the mRNA expressed in muscle, we first generated animals that express Flag::PAB-1 in non-pharyngeal muscles from an integrated transgene using the myo-3 promoter5. The mRNA-Flag::PAB-1 complex was co-immunoprecipitated from cell lysate using anti-Flag monoclonal antibodies.
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11542.gif

source_name: Pre-IP

tag: Pre-IP

source_name: Post-IP

tag: Post-IP


title: 3 hr ameba + caco  5 5 03

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40381.gif

source_name: 12ug 3hr Amebic + caco RNA

tag: 12ug 3hr Amebic + caco RNA


title: DBYyap1- + 0.3 mM H2O2 (20 min) b

description:
Simple annotation: Stress, H2O2
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/692.gif

source_name: time = 0 min

tag: time = 0 min

source_name: time = 20 min

tag: time = 20 min


title: mixed stage N2 (red, channel 2) vs. SL2-amplified N2 (repeat #3) (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11393.gif

source_name: mixed stage N2 (red, channel 2)

tag: mixed stage N2 (red, channel 2)


title: mixed stage N2 (red, channel 2) vs. SL2-amplified N2 (repeat #4) (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11395.gif


title: mixed stage N2 (red, channel 2) vs. SL2-amplified N2 (repeat #2) (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11391.gif


title: DY (zap1) 3 mM vs. 61 nM zinc

status: Public on Jul 21 2005

description:
Simple annotation: Metals, Zinc
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/825.gif

source_name: 61 nM zinc

tag: 61 nM zinc

source_name: 3 mM zinc

tag: 3 mM zinc


title: DY1457 (wild type) 10 uM zinc vs. 3 mM

description:
Simple annotation: Metals, Zinc
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/824.gif

source_name: 10 uM zinc

tag: 10 uM zinc


title: DY1457 (wild type) 3 mM vs. 61 nM zinc

description:
Simple annotation: Metals, Zinc
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/819.gif


title: mixed stage N2 (red, channel 2) vs. SL2-amplified N2 (repeat #1) (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11389.gif


title: Transient transfection of SW-13 cells with BRG1 (1)

description:
Simple annotation: Cell-line, SW13
Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3583.gif

organism: Homo sapiens


title: DY zap1 3 mM vs. 10 uM zinc #2

description:
Simple annotation: Metals, Zinc
Image: http://smd.stanford.edu/MicroArray/gifs/1999-11/1108.gif

source_name: 76 nM zinc

tag: 76 nM zinc


title: DY1457 (wild type) 3 mM vs. 76 nM zinc

description:
Simple annotation: Metals, Zinc
Image: http://smd.stanford.edu/MicroArray/gifs/1999-11/1139.gif


title: wild type vs. zap1 - 76 nM zinc

description:
Simple annotation: Metals, Zinc
Image: http://smd.stanford.edu/MicroArray/gifs/1999-11/1104.gif

source_name: wild type

tag: wild type


title: N2 control #2 (red, channel 2) vs. estrogen 10e-05 (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs//10420.gif

source_name: estrogen 10e-05 (green)

tag: estrogen 10e-05 (green)

source_name: N2 control #2 (red)

tag: N2 control #2 (red)


title: wt vs zap1 - 61 nM zinc

description:
Simple annotation: Metals, Zinc
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/827.gif

source_name: zap1 in 61 nM zinc

tag: zap1 in 61 nM zinc

source_name: wt in 61 nM zinc

tag: wt in 61 nM zinc


title: N2 control #1 (red, channel 2) vs. testosterone 10e-09 (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10416.gif

source_name: testosterone 10e-09 (green)

tag: testosterone 10e-09 (green)

source_name: N2 control #1 (red)

tag: N2 control #1 (red)


title: DY zap1 3 mM vs. 76 nM zinc

description:
Simple annotation: Metals, Zinc
Image: http://smd.stanford.edu/MicroArray/gifs/1999-11/1106.gif


title: N2 control #1 (red, channel 2) vs. progesterone 10e-07 (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10418.gif

source_name: progesterone 10e-07 (green)

tag: progesterone 10e-07 (green)


title: N2 control #2 (red, channel 2) vs. cholesterol 10e-09 (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10422.gif

source_name: cholesterol 10e-09 (green)

tag: cholesterol 10e-09 (green)


title: N2 control #1 (red, channel 2) vs. progesterone 10e-09 (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10417.gif

source_name: progesterone 10e-09 (green)

tag: progesterone 10e-09 (green)


title: N2 control #2 (red, channel 2) vs. progesterone 10e-05 (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10423.gif

source_name: progesterone 10e-05 (green)

tag: progesterone 10e-05 (green)


title: 6hr ameba alone  5 5 03

description:
Simple annotation: Enteric environment, Enterocyte interaction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40382.gif

source_name: pHos PCR reference M13F M13R (1x)

tag: pHos PCR reference M13F M13R (1x)

source_name: 8ug 6hr Amebic RNA

tag: 8ug 6hr Amebic RNA


title: U2 Comp 07 hr 10 min Uracil Batch vs Chemostat Comparison

status: Public on Jul 16 2005

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42222.gif

source_name: 07 hr 10 min Uracil Batch Expriment #2 (4/28/3)

source_name: Uracil limited chemostat

tag: Uracil limited chemostat


title: Transient transfection of SW-13 cells with BRG1 (2)

description:
Simple annotation: Cell-line, SW13
Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3581.gif


title: DY1457 (wild type) 3 mM vs. 10 uM zinc

description:
Simple annotation: Metals, Zinc
Image: http://smd.stanford.edu/MicroArray/gifs/1999-11/1155.gif

source_name: 3 mM zinc

tag: 3 mM zinc

source_name: 61 nM zinc

tag: 61 nM zinc


title: hif-1 (red, channel 2) vs.hif-1; vhl-1 (green, channel 1) repeat no. 1

status: Public on Jul 20 2005

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27320.gif

source_name: hif-1; vhl-1

tag: hif-1; vhl-1


title: Transient transfection of SW-13 cells with BRG1 (3)

description:
Simple annotation: Cell-line, SW13
Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3793.gif


title: L2 CompR 12 hr 03 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42400.gif

source_name: 12 hr 03 min Leucine Batch Expriment #4

tag: 12 hr 03 min Leucine Batch Expriment #4

source_name: "Leucine limited chemostat, with matching OD"


title: U2 Comp 06 hr 05 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42221.gif

source_name: 06 hr 05 min Uracil Batch Expriment #2 (4/28/3)


title: U2 Comp 05 hr 15 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42218.gif

source_name: 05 hr 00 min Uracil Batch Expriment #2 (4/28/3)


title: L2 CompR 09 hr 58 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42398.gif

source_name: 09 hr 58 min Leucine Batch Expriment #4

tag: 09 hr 58 min Leucine Batch Expriment #4

tag: "Leucine limited chemostat, with matching OD"


title: wild-type (red, channel 2) vs. VHL mutant (ok161) (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11704.gif

source_name: VHL mutant (ok161) (green)

tag: VHL mutant (ok161) (green)

source_name: wild-type control (red)

tag: wild-type control (red)


title: hif-1 (red, channel 2) vs. hif-1; vhl-1 (green, channel 1) repeat no. 2

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27321.gif


title: L2 CompR 11 hr 04 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42399.gif

source_name: 11 hr 04 min Leucine Batch Expriment #4

tag: 11 hr 04 min Leucine Batch Expriment #4


title: hif-1 (red, channel 2) vs. hif-1; vhl-1 (green, channel 1) repeat no. 3

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27322.gif


title: L2 CompR 05 hr 58 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42393.gif

source_name: 05 hr 58 min Leucine Batch Expriment #4

tag: 05 hr 58 min Leucine Batch Expriment #4


title: L2 CompR 06 hr 58 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42394.gif

source_name: 06 hr 58 min Leucine Batch Expriment #4

tag: 06 hr 58 min Leucine Batch Expriment #4


title: L2 CompR 08 hr 58 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42396.gif

source_name: 08 hr 58 min Leucine Batch Expriment #4

tag: 08 hr 58 min Leucine Batch Expriment #4


title: CC PU 3A Phosphate-Uracil Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42369.gif

source_name: Phosphate Chemostat

tag: Phosphate Chemostat


title: L2 CompR 07 hr 58 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42395.gif

source_name: 07 hr 58 min Leucine Batch Expriment #4

tag: 07 hr 58 min Leucine Batch Expriment #4


title: CC LS 1A Leucine-Sulfate Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42391.gif

source_name: Leucine limited chemostat

tag: Leucine limited chemostat

source_name: Sulfate limited chemostat

tag: Sulfate limited chemostat


title: L2 CompR 05 hr 00 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42392.gif

source_name: 05 hr 00 min Leucine Batch Expriment #4

tag: 05 hr 00 min Leucine Batch Expriment #4


title: CC LS 1B Leucine-Sulfate Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42390.gif


title: U3Comp 09 hr 10 min Uracil Batch vs Chemostat Comparison (rescan)

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42061.gif

source_name: 09 hr 10 min Uracil Batch

tag: 09 hr 10 min Uracil Batch

source_name: Uracil limited chemostat

tag: Uracil limited chemostat


title: CC UL 1A Uracil-Leucine Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42388.gif


title: U3Comp 25 hr 55 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42066.gif

source_name: 25 hr 55 min Uracil Batch

tag: 25 hr 55 min Uracil Batch


title: CC UL 1B Uracil-Leucine Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42386.gif


title: CC PU 1B Phosphate-Uracil Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42383.gif


title: U3Comp 13 hr 30 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42065.gif

source_name: 13 hr 30 min Uracil Batch

tag: 13 hr 30 min Uracil Batch


title: U3Comp 10 hr 08 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42062.gif

source_name: 10 hr 08 min Uracil Batch

tag: 10 hr 08 min Uracil Batch


title: U3Comp 11 hr 10 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42063.gif

source_name: 11 hr 10 min Uracil Batch

tag: 11 hr 10 min Uracil Batch


title: CC LS 2A Leucine-Sulfate Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42382.gif


title: L2 Comp 24 hr 59 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42200.gif

source_name: 24 hr 59 min Leucine Batch Expriment #4

tag: 24 hr 59 min Leucine Batch Expriment #4

source_name: "Leucine limited chemostat, with matching OD"


title: CC LS 2B Leucine-Sulfate Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42381.gif


title: CC PU 1A Phosphate-Uracil Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42385.gif


title: U3Comp 08 hr 08 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42059.gif

source_name: 08 hr 08 min Uracil Batch

tag: 08 hr 08 min Uracil Batch


title: U3Comp 07 hr 15 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42057.gif

source_name: 07 hr 15 min Uracil Batch

tag: 07 hr 15 min Uracil Batch


title: U3Comp 12 hr 10 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42064.gif

source_name: 12 hr 10 min Uracil Batch

tag: 12 hr 10 min Uracil Batch


title: CC UL 2A Uracil-Leucine Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42380.gif


title: U2 Comp 31 hr 35 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42231.gif

source_name: 31 hr 35 min Uracil Batch Expriment #2 (4/28/3)


title: L1CompR 21 hr 10 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42052.gif

source_name: 21 hr 10 min Leucine Batch

tag: 21 hr 10 min Leucine Batch

tag: "Leucine limited chemostat, with matching OD"


title: U3Comp 06 hr 05 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42056.gif

source_name: 06 hr 05 min Uracil Batch

tag: 06 hr 05 min Uracil Batch


title: L2 Comp 12 hr 59 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42199.gif

source_name: 12 hr 59 min Leucine Batch Expriment #4

tag: 12 hr 59 min Leucine Batch Expriment #4


title: L1CompR 18 hr 10 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42051.gif

source_name: 18 hr 10 min Leucine Batch

tag: 18 hr 10 min Leucine Batch


title: L1CompR 15 hr 00 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42050.gif

source_name: 15 hr 00 min Leucine Batch

tag: 15 hr 00 min Leucine Batch


title: L1CompR 26 hr 40 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42053.gif

source_name: 26 hr 40 min Leucine Batch

tag: 26 hr 40 min Leucine Batch


title: L2 Comp 12 hr 03 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42198.gif

source_name: 12 hr 03 min Leucine Batch Expriment #4

tag: 12 hr 03 min Leucine Batch Expriment #4


title: CC LS 3A Leucine-Sulfate Chemostat Comparison (scanner1)

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42377.gif

source_name: Leucine limited chemostat

tag: Leucine limited chemostat

source_name: Sulfate limited chemostat

tag: Sulfate limited chemostat


title: CC PU 2A Phosphate-Uracil Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42378.gif

source_name: Phosphate Chemostat

tag: Phosphate Chemostat

source_name: Uracil limited chemostat

tag: Uracil limited chemostat


title: U3Comp 05 hr 10 min Uracil Batch vs Chemostat Comparison (rescan)

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42055.gif

source_name: 05 hr 10 min Uracil Batch

tag: 05 hr 10 min Uracil Batch


title: L2 Comp 11 hr 04 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42197.gif

source_name: 11 hr 04 min Leucine Batch Expriment #4

tag: 11 hr 04 min Leucine Batch Expriment #4

source_name: "Leucine limited chemostat, with matching OD"


title: L2 Comp 09 hr 58 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42196.gif

source_name: 09 hr 58 min Leucine Batch Expriment #4

tag: 09 hr 58 min Leucine Batch Expriment #4


title: CC UL 2B Uracil-Leucine Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42379.gif


title: L2 Comp 07 hr 58 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42194.gif

source_name: 07 hr 58 min Leucine Batch Expriment #4

tag: 07 hr 58 min Leucine Batch Expriment #4


title: CC UL 3B Uracil-Leucine Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42373.gif


title: CC PU 3B Phosphate-Uracil Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42370.gif


title: L2 Comp 06 hr 58 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42193.gif

source_name: 06 hr 58 min Leucine Batch Expriment #4

tag: 06 hr 58 min Leucine Batch Expriment #4


title: L2 Comp 08 hr 58 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42195.gif

source_name: 08 hr 58 min Leucine Batch Expriment #4

tag: 08 hr 58 min Leucine Batch Expriment #4


title: CC UL 3A Uracil-Leucine Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42372.gif


title: L2 Comp 05 hr 58 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42192.gif

source_name: 05 hr 58 min Leucine Batch Expriment #4

tag: 05 hr 58 min Leucine Batch Expriment #4

tag: "Leucine limited chemostat, with matching OD"


title: P1Comp 15 hr 0 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27099.gif

source_name: Phosphate limited chemostat

tag: Phosphate limited chemostat

source_name: 15 hr 0min Phosphate limited batch

tag: 15 hr 0min Phosphate limited batch


title: L1CompR 13 hr 10 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42049.gif

source_name: 13 hr 10 min Leucine Batch

tag: 13 hr 10 min Leucine Batch


title: P1Comp 13 hr 15 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27098.gif

source_name: 13 hr 15min Phosphate limited batch

tag: 13 hr 15min Phosphate limited batch


title: U2 Comp 13 hr 05 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42229.gif

source_name: 13 hr 05 min Uracil Batch Expriment #2 (4/28/3)


title: P1Comp 11 hr 10 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27097.gif

source_name: 11 hr 10min Phosphate limited batch

tag: 11 hr 10min Phosphate limited batch


title: P1Comp 05 hr 5 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27095.gif

source_name: 5 hr 5min Phosphate limited batch

tag: 5 hr 5min Phosphate limited batch


title: CC LS 3B Leucine-Sulfate Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42375.gif

source_name: Sulfate limited chemostat

tag: Sulfate limited chemostat

source_name: Leucine limited chemostat

tag: Leucine limited chemostat


title: P1Comp 19 hr 6 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27096.gif

source_name: 19 hr 6min Phosphate limited batch

tag: 19 hr 6min Phosphate limited batch


title: L2 Comp 05 hr 00 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42191.gif

source_name: 05 hr 00 min Leucine Batch Expriment #4

tag: 05 hr 00 min Leucine Batch Expriment #4


title: U2 Comp 11 hr 05 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42227.gif

source_name: 11 hr 05 min Uracil Batch Expriment #2 (4/28/3)

source_name: Uracil limited chemostat

tag: Uracil limited chemostat


title: L1CompR 11 hr 10 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42048.gif

source_name: 11 hr 10 min Leucine Batch

tag: 11 hr 10 min Leucine Batch

source_name: "Leucine limited chemostat, with matching OD"


title: CC PU 2B Phosphate-Uracil Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42404.gif

source_name: Phosphate Chemostat

tag: Phosphate Chemostat


title: P2Comp 12 hr 22 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28852.gif

source_name: 12 hr 22min Phosphate limited batch

tag: 12 hr 22min Phosphate limited batch


title: U2 Comp 10 hr 05 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42226.gif

source_name: 10 hr 05 min Uracil Batch Expriment #2 (4/28/3)


title: U2 Comp 08 hr 10 min Uracil Batch vs Chemostat Comparison (rescan)

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42224.gif

source_name: 08 hr 05 min Uracil Batch Expriment #2 (4/28/3)


title: P2Comp 25 hr 43 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28857.gif

source_name: Phosphate limited chemostat

source_name: 25 hr 43min Phosphate limited batch

tag: 25 hr 43min Phosphate limited batch


title: P1Comp 09 hr 10 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27094.gif

source_name: 9 hr 10min Phosphate limited batch

tag: 9 hr 10min Phosphate limited batch


title: L1CompR 07 hr 05 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42046.gif

source_name: 07 hr 05 min Leucine Batch

tag: 07 hr 05 min Leucine Batch

tag: "Leucine limited chemostat, with matching OD"


title: U2 Comp 12 hr 05 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42228.gif

source_name: 12 hr 05 min Uracil Batch Expriment #2 (4/28/3)


title: P2Comp 11 hr 51 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28851.gif

tag: Phosphate limited chemostat

source_name: 11 hr 51min Phosphate limited batch

tag: 11 hr 51min Phosphate limited batch


title: L1CompR 09 hr 05 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42047.gif

source_name: 09 hr 05 min Leucine Batch

tag: 09 hr 05 min Leucine Batch


title: U2 Comp 09 hr 12 min Uracil Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42225.gif

source_name: 09 hr 12 min Uracil Batch Expriment #2 (4/28/3)


title: P2Comp 09 hr 36 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28844.gif

source_name: 9 hr 36min Phosphate limited batch

tag: 9 hr 36min Phosphate limited batch


title: P2Comp 19 hr 45 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28854.gif

source_name: 19 hr 45min Phosphate limited batch

tag: 19 hr 45min Phosphate limited batch


title: P2Comp 09 hr 49 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28845.gif

source_name: 9 hr 49min Phosphate limited batch

tag: 9 hr 49min Phosphate limited batch


title: P2Comp 10 hr 20 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28847.gif

source_name: 10 hr 20min Phosphate limited batch

tag: 10 hr 20min Phosphate limited batch


title: L1CompR 05 hr 15 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42045.gif

source_name: 05 hr 15 min Leucine Batch

tag: 05 hr 15 min Leucine Batch

source_name: "Leucine limited chemostat, with matching OD"


title: L2 CompR 12 hr 59 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42401.gif

source_name: 12 hr 59 min Leucine Batch Expriment #4

tag: 12 hr 59 min Leucine Batch Expriment #4


title: S4Comp 14 hr 05 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34883.gif

source_name: Sulfate limited chemostat

tag: Sulfate limited chemostat

source_name: 14 hr 05 min Sulfate Batch

tag: 14 hr 05 min Sulfate Batch


title: P1Comp 33 hr 5 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27106.gif

source_name: Phosphate limited chemostat

source_name: 33 hr 5min Phosphate limited batch

tag: 33 hr 5min Phosphate limited batch


title: P2Comp 10 hr 50 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28849.gif

source_name: 10 hr 50min Phosphate limited batch

tag: 10 hr 50min Phosphate limited batch


title: S4Comp 15 hr 05 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34884.gif

source_name: 15 hr 05 min Sulfate Batch

tag: 15 hr 05 min Sulfate Batch


title: S4Comp 13 hr 05 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34882.gif

source_name: 13 hr 05 min Sulfate Batch

tag: 13 hr 05 min Sulfate Batch


title: L2 CompR 24 hr 59 min Leucine Batch vs Chemostat Comparison

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42402.gif

source_name: 24 hr 59 min Leucine Batch Expriment #4

tag: 24 hr 59 min Leucine Batch Expriment #4


title: P2Comp 10 hr 35 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28848.gif

source_name: 10 hr 35min Phosphate limited batch

tag: 10 hr 35min Phosphate limited batch


title: S4Comp 34 hr 20 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34885.gif

source_name: 34 hr 20 min Sulfate Batch

tag: 34 hr 20 min Sulfate Batch


title: P2Comp 10 hr 5 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28846.gif

tag: Phosphate limited chemostat

source_name: 10 hr 5min Phosphate limited batch

tag: 10 hr 5min Phosphate limited batch


title: DTU Pulse Chase 2 2hr a

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44109.gif

organism: Toxoplasma gondii

source_name: rna ref

tag: rna ref

source_name: equal fraction SH-U purified

tag: equal fraction SH-U purified


title: P1Comp 27 hr 15 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27105.gif

source_name: 27 hr 15min Phosphate limited batch

tag: 27 hr 15min Phosphate limited batch


title: DTU Pulse Chase 1 0hr

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42640.gif

source_name: DTU mRNA purified after 1hr pulse

tag: DTU mRNA purified after 1hr pulse


title: DTU Pulse Chase 1 6hr

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42657.gif

source_name: DTU purified 6hr chase, equal fraction to t=0


title: S4Comp 11 hr 00 min Sulfate Batch vs Chemostat Comparison (rescan)

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34881.gif

source_name: 11 hr 00 min Sulfate Batch

tag: 11 hr 00 min Sulfate Batch


title: P2Comp 08 hr 48 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28842.gif

source_name: 8 hr 48min Phosphate limited batch

tag: 8 hr 48min Phosphate limited batch


title: DTU Pulse Chase 2 1hr a

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44108.gif


title: P2Comp 09 hr 20 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28843.gif

source_name: 9 hr 20min Phosphate limited batch

tag: 9 hr 20min Phosphate limited batch


title: CC SP 3B  Sulfate-Phosphate Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37285.gif

source_name: Phosphate limited chemostat

source_name: Sulfate limited chemostat

tag: Sulfate limited chemostat


title: DTU Bradyzoite Pulse chase 1 0hr

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53866.gif

source_name: ref

tag: ref

source_name: BZ pc 1 1 hr pulse, 0 hr chase

tag: BZ pc 1 1 hr pulse, 0 hr chase


title: CC SP 1B  Sulfate-Phosphate Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37282.gif


title: P1Comp 45 hr 5 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27108.gif

source_name: 45 hr 5min Phosphate limited batch

tag: 45 hr 5min Phosphate limited batch


title: P1Comp 24 hr 5 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27103.gif

source_name: 24 hr 5min Phosphate limited batch

tag: 24 hr 5min Phosphate limited batch


title: DTU Pulse Chase 2 0hr a

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44107.gif

source_name: SH-U purified

tag: SH-U purified


title: DTU Pulse Chase 2 6hr b

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44195.gif

source_name: sh-u purified mRNA, equiv fraction

tag: sh-u purified mRNA, equiv fraction


title: DTU Bradyzoite Pulse chase 1 2hr

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53864.gif

source_name: BZ pulse-chase 1, 2 hr chase

tag: BZ pulse-chase 1, 2 hr chase


title: P2Comp 08 hr 19 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28841.gif

tag: Phosphate limited chemostat

source_name: 8 hr 19min Phosphate limited batch

tag: 8 hr 19min Phosphate limited batch


title: DTU Bradyzoite Pulse-chase 2 2hr

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/54836.gif

source_name: SH-mRNA, 2 hr chase

tag: SH-mRNA, 2 hr chase


title: S4Comp 10 hr 00 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34879.gif

source_name: 10 hr 00 min Sulfate Batch

tag: 10 hr 00 min Sulfate Batch


title: CC SP 3A  Sulfate-Phosphate Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37281.gif


title: P1Comp 21 hr 5 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27102.gif

source_name: 21 hr 5min Phosphate limited batch

tag: 21 hr 5min Phosphate limited batch


title: P2Comp 07 hr 47 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28840.gif

source_name: 7 hr 47min Phosphate limited batch

tag: 7 hr 47min Phosphate limited batch


title: P1Comp 07 hr 5 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27101.gif

source_name: 7 hr 5min Phosphate limited batch

tag: 7 hr 5min Phosphate limited batch


title: DTU Bradyzoite Pulse-chase 2 0hr

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/54835.gif

source_name: 0 hr SH-mRNA, 1 hr pulse

tag: 0 hr SH-mRNA, 1 hr pulse


title: S4Comp 08 hr 05 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34877.gif

source_name: 08 hr 05 min Sulfate Batch

tag: 08 hr 05 min Sulfate Batch


title: DTU Pulse Chase 2 2hr b

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44193.gif

source_name: rna ref

tag: rna ref


title: S4Comp 09 hr 00 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34878.gif

source_name: Sulfate limited chemostat

tag: Sulfate limited chemostat

source_name: 09 hr 00 min Sulfate Batch

tag: 09 hr 00 min Sulfate Batch


title: DTU Pulse Chase 2 0hr b

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45090.gif

source_name: equal fraction elluted

tag: equal fraction elluted


title: P2Comp 06 hr 15 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28838.gif

source_name: Phosphate limited chemostat

source_name: 6 hr 15min Phosphate limited batch

tag: 6 hr 15min Phosphate limited batch


title: S4Comp 07 hr 10 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34876.gif

source_name: 07 hr 10 min Sulfate Batch

tag: 07 hr 10 min Sulfate Batch


title: P2Comp 07 hr 15 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28839.gif

source_name: 7 hr 15min Phosphate limited batch

tag: 7 hr 15min Phosphate limited batch


title: DTU Pulse Chase 1 1hr

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42973.gif

source_name: 1hr chase, equal fraction elluted mRNA to zero timepoint


title: DTU Pulse Chase 2 6hr a

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44110.gif

source_name: equal fraction SH-U purified

tag: equal fraction SH-U purified


title: Tachy Synthesis 2b

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44298.gif

source_name: SH-U mRNA (150 ng)

tag: SH-U mRNA (150 ng)


title: Tachy Abundance 1b

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44295.gif

source_name: total mRNA

tag: total mRNA


title: Tachy Abundance 1a

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44291.gif


title: DTU Pulse Chase 2 1hr b

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44191.gif

source_name: sh-u purified mRNA, equiv fraction

tag: sh-u purified mRNA, equiv fraction


title: Tachy Synthesis 2a

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44296.gif


title: S4Comp 06 hr 05 min Sulfate Batch vs Chemostat Comparison (rescan)

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34874.gif

source_name: 06 hr 05 min Sulfate Batch

tag: 06 hr 05 min Sulfate Batch


title: P1Comp 16 hr 55 min Phosphate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27100.gif

tag: Phosphate limited chemostat

source_name: 16 hr 55min Phosphate limited batch

tag: 16 hr 55min Phosphate limited batch


title: Brady Synthesis 1b

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44533.gif

source_name: DTU mRNA

tag: DTU mRNA


title: DTU Pulse Chase 1 2hr

description:
Simple annotation: Transcription, RNA stability
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50145.gif

source_name: DTU purified 2 hr chase, equal fraction to t=0


title: CC SP 2B  Sulfate-Phosphate Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37284.gif


title: P2Comp 04 hr 15 min Phosphate Batch vs Chemostat Comparison2

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28837.gif

source_name: 4 hr 10min Phosphate limited batch

tag: 4 hr 10min Phosphate limited batch


title: CC SP 1A  Sulfate-Phosphate Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37279.gif

source_name: Sulfate limited chemostat


title: S4Comp 05 hr 00 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34872.gif

source_name: 05 hr 00 min Sulfate Batch

tag: 05 hr 00 min Sulfate Batch


title: GSY11A

type: genomic

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48037.gif

molecule: genomic DNA

source_name: S288C sonicated genomic DNA 4ug

tag: S288C sonicated genomic DNA 4ug

source_name: GSY11 sonicated DNA 4 ug

tag: GSY11 sonicated DNA 4 ug


title: GSY1A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48029.gif

source_name: GSY1 sonicated DNA 4 ug

tag: GSY1 sonicated DNA 4 ug


title: GSY12A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48039.gif

source_name: GSY12 sonicated DNA 4 ug

tag: GSY12 sonicated DNA 4 ug


title: GSY3B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48034.gif

source_name: GSY3 sonicated DNA 4 ug

tag: GSY3 sonicated DNA 4 ug


title: mOb 24hr 2%

description:
Simple annotation: Hypoxia, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/46174.gif

organism: Mus musculus

source_name: 21% x 24 hour mOb

tag: 21% x 24 hour mOb

source_name: 2% 24 hours

tag: 2% 24 hours


title: S1Comp 24 hr 10 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32633.gif

tag: Sulfate limited chemostat

source_name: 24 hr 10 min Sulfate limited batch

tag: 24 hr 10 min Sulfate limited batch


title: GSY10B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48036.gif

source_name: GSY10 sonicated DNA 4 ug

tag: GSY10 sonicated DNA 4 ug


title: GSY2B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48032.gif

source_name: GSY2 sonicated DNA 4 ug

tag: GSY2 sonicated DNA 4 ug


title: Brady Synthesis 2b

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44534.gif

source_name: rna ref

tag: rna ref


title: GSY3A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48033.gif


title: GSY11B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48038.gif


title: S1Comp 22 hr 05 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32632.gif

source_name: 22 hr 05 min Sulfate limited batch

tag: 22 hr 05 min Sulfate limited batch


title: Brady Abundance 1a

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44181.gif

source_name: total mRNA

tag: total mRNA


title: GSY2A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48031.gif


title: Brady Abundance 2a

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44180.gif


title: mOb 24hr 0%

description:
Simple annotation: Hypoxia, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/46175.gif


title: GSY1B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48030.gif


title: GSY10A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48035.gif


title: Tachy Abundance 2b

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38663.gif

source_name: mRNA

tag: mRNA


title: Brady Abundance 1b

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44400.gif


title: S1Comp 20 hr 10 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32631.gif

source_name: 20 hr 10 min Sulfate limited batch

tag: 20 hr 10 min Sulfate limited batch


title: GSY12B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48040.gif


title: Brady Synthesis 1a

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44026.gif

source_name: DTU mRNA

tag: DTU mRNA


title: CC SP 2A  Sulfate-Phosphate Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37280.gif

source_name: Sulfate limited chemostat

source_name: Phosphate limited chemostat

tag: Phosphate limited chemostat


title: S1Comp 15 hr 20 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32629.gif

source_name: 15 hr 20 min Sulfate limited batch

tag: 15 hr 20 min Sulfate limited batch


title: Tachy Synthesis 1b

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38662.gif

source_name: purified mRNA

tag: purified mRNA


title: S1Comp 18 hr 00 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32630.gif

source_name: 18 hr 00 min Sulfate limited batch

tag: 18 hr 00 min Sulfate limited batch


title: Tachy Abundance 2a

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35759.gif

source_name: Total mRNA

tag: Total mRNA


title: GSY5-A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs//48279.gif

source_name: S288C sonicated genomic DNA 4 ug

tag: S288C sonicated genomic DNA 4 ug

source_name: GSY5 sonicated genomic DNA 4 ug

tag: GSY5 sonicated genomic DNA 4 ug


title: GSY9-B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48288.gif

source_name: GSY9 sonicated genomic DNA 4 ug

tag: GSY9 sonicated genomic DNA 4 ug


title: GSY8-B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48286.gif

source_name: GSY8 sonicated genomic DNA 4 ug

tag: GSY8 sonicated genomic DNA 4 ug


title: S1Comp 12 hr 57 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32628.gif

tag: Sulfate limited chemostat

source_name: 12 hr 57 min Sulfate limited batch

tag: 12 hr 57 min Sulfate limited batch


title: GSY8-A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48285.gif


title: GSY4-A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48277.gif

source_name: GSY4 sonicated genomic DNA 4 ug

tag: GSY4 sonicated genomic DNA 4 ug


title: GSY4-B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs//48278.gif


title: S1Comp 11 hr 10 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32627.gif

source_name: 11 hr 10 min Sulfate limited batch

tag: 11 hr 10 min Sulfate limited batch


title: S1Comp 07 hr 05 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32624.gif

source_name: 07 hr 05 min Sulfate limited batch

tag: 07 hr 05 min Sulfate limited batch


title: GSY6-B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48282.gif

source_name: GSY6 sonicated genomic DNA 4 ug

tag: GSY6 sonicated genomic DNA 4 ug


title: GSY6-A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48281.gif


title: GSY9-A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48287.gif


title: GSY5-B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48280.gif


title: GSY7-B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48284.gif

source_name: GSY7 sonicated genomic DNA 4 ug

tag: GSY7 sonicated genomic DNA 4 ug


title: Tachy Synthesis 1a

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35758.gif

source_name: rna ref

tag: rna ref

source_name: SH-U purified mRNA

tag: SH-U purified mRNA


title: S1Comp 08 hr 55 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32626.gif

source_name: Sulfate limited chemostat

source_name: 08 hr 55 min Sulfate limited batch

tag: 08 hr 55 min Sulfate limited batch


title: GSY7-A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48283.gif


title: Brady Synthesis 2a

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44030.gif

source_name: DTU mRNA

tag: DTU mRNA


title: S1Comp 05 hr 10 min Sulfate Batch vs Chemostat Comparison

description:
Simple annotation: Nutrient effects, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32622.gif

source_name: 05 hr 10 min Sulfate limited batch

tag: 05 hr 10 min Sulfate limited batch


title: Brady Abundance 2b

description:
Simple annotation: Transcription, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/44399.gif

source_name: total mRNA

tag: total mRNA


title: Sucrose (0-->1M) 90 min

status: Public on Jul 12 2005

description:
Simple annotation: Stress, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35617.gif

organism: Streptomyces coelicolor

source_name: time zero

tag: time zero

source_name: 90 min

tag: 90 min


title: Sucrose (0-->1M) SMM 15 min

description:
Simple annotation: Stress, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35613.gif

source_name: 15 min

tag: 15 min


title: Phosphate upshift 90 min (repeat)

description:
Simple annotation: Stress, Polyphosphate
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33549.gif


title: gDNA M145 vs RNA M600 R5 (-sucrose) OD 1.0

type: mixed

description:
Simple annotation: Transcription, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48215.gif

source_name: gDNA M145

tag: gDNA M145

source_name: RNA M600 R5 (-sucrose) OD 0

tag: RNA M600 R5 (-sucrose) OD 0


title: UPRT + HeLa Response to DTU

description:
Simple annotation: Transcription, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/46161.gif

source_name: HeLa

tag: HeLa

source_name: UPRT + HeLa

tag: UPRT + HeLa


title: Phosphate upshift 45 min (repeat)

description:
Simple annotation: Stress, Polyphosphate
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33547.gif

source_name: 45 min

tag: 45 min


title: Phosphate upshift 60 min (repeat)

description:
Simple annotation: Stress, Polyphosphate
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33548.gif

source_name: 60 min

tag: 60 min


title: Sucrose (0-->1M) 30 min

description:
Simple annotation: Stress, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35614.gif

source_name: 30 min

tag: 30 min


title: U373MG response to DTU

description:
Simple annotation: Transcription, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56410.gif

source_name: wildtype

tag: wildtype

source_name: UPRT+

tag: UPRT+


title: Sucrose (0-->1M) 45 min

description:
Simple annotation: Stress, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35615.gif


title: gDNA M600 vs RNA M600 SMM(control) OD0.5

description:
Simple annotation: Transcription, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48212.gif

source_name: gDNA M600

tag: gDNA M600

source_name: RNA M600 SMM(control) OD5

tag: RNA M600 SMM(control) OD5


title: 30--37C R5 Repeat2 90 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34274.gif


title: Phosphate upshift 30 min (repeat)

description:
Simple annotation: Stress, Polyphosphate
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33546.gif


title: control SMM (spin) 60 min

description:
Simple annotation: Stress, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35533.gif


title: gDNA M600 vs RNA OD1 R5 (from 30-->37C R5 repeat)

description:
Simple annotation: Stress, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34275.gif

source_name: RNA OD 1 R5 time zero from 30-->37C Repeat 10/23/02


title: control SMM (spin) 30 min

description:
Simple annotation: Stress, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35531.gif


title: gDNA M600 vs RNA M600 R5 (EtOH) OD 1.0

description:
Simple annotation: Transcription, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48213.gif

source_name: RNA M600 R5 (EtOH) OD 0

tag: RNA M600 R5 (EtOH) OD 0


title: control SMM (spin) 45 min

description:
Simple annotation: Stress, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35532.gif


title: Sucrose (0-->1M) 60 min

description:
Simple annotation: Stress, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35616.gif


title: gDNA M145 vs RNA M600 R5 (EtOH) OD 1.0

description:
Simple annotation: Transcription, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48214.gif


title: 30-->42C 30 min repeat

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32910.gif


title: 30-->42C 45 min repeat

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32911.gif


title: Heat shock 37C SMM 30 min 0403

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50495.gif

source_name: time zero OD 5

tag: time zero OD 5


title: 30-->42C 60 min repeat

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32912.gif

source_name: time zero


title: M145 R5 OD 1 (12 hr)  vs 45 hr

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49664.gif

source_name: 45 hr

tag: 45 hr


title: Heat shock 37C SMM 15 min 0403

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50494.gif

source_name: 15 min


title: M145 R5 OD 1 (12 hr)  vs 34 hr

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49660.gif

source_name: 34 hr

tag: 34 hr


title: M145 R5 OD 1 (12 hr)  vs 40 hr

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49662.gif

source_name: 40 hr

tag: 40 hr


title: Heat shock 37C SMM 5 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50492.gif

source_name: 5 min

tag: 5 min


title: control SMM (spin) 15 min

description:
Simple annotation: Stress, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35530.gif

tag: time zero

tag: 15 min


title: Ethanol 5% 90 min (R5 M600)

description:
Simple annotation: Stress, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33897.gif

source_name: 90 min

tag: 90 min


title: 30-->42C 90 min repeat

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32913.gif


title: Ethanol 5% 45 min (R5 M600)

description:
Simple annotation: Stress, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33895.gif

source_name: 45 min


title: RNA M600 R5 (EtOH) OD 1.0 vs RNA M600 SMM (control) OD 0.5

description:
Simple annotation: Transcription, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48357.gif

source_name: RNA M600 SMM (control) OD5

tag: RNA M600 SMM (control) OD5


title: M145 R5 OD 1 (12 hr)  vs 16 hr

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49655.gif

source_name: 16 hr

tag: 16 hr


title: Phosphate upshift 15 min (repeat)

description:
Simple annotation: Stress, Polyphosphate
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33545.gif


title: Ethanol 5% 15 min (R5 M600)

description:
Simple annotation: Stress, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33893.gif


title: Ethanol 5% 30 min (R5 M600)

description:
Simple annotation: Stress, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33894.gif

source_name: 30 min


title: control SMM 60 min

description:
Simple annotation: Stress, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35528.gif

source_name: 60 min

tag: 60 min


title: Ethanol 5% 60 min (R5 M600)

description:
Simple annotation: Stress, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33896.gif


title: control SMM 90 min

description:
Simple annotation: Stress, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35529.gif


title: Heat shock 37C SMM 10 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50493.gif

source_name: 10 min

tag: 10 min


title: M145 R5 OD 1 (12 hr)  vs 24 hr

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49659.gif

source_name: 24 hr

tag: 24 hr


title: Control R5 M600 90 min

description:
Simple annotation: Stress, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34220.gif


title: control SMM (spin) 90 min

description:
Simple annotation: Stress, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35534.gif


title: control SMM 30 min

description:
Simple annotation: Stress, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35526.gif

tag: 30 min


title: M145 R5 OD 1 (12 hr)  vs M600 R5 OD 1(10hr)

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49654.gif


title: control SMM 45 min

description:
Simple annotation: Stress, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35527.gif

tag: 45 min


title: M145 R5 OD 1 (12 hr)  vs 20 hr

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49657.gif

source_name: 20 hr

tag: 20 hr


title: control SMM 15 min

description:
Simple annotation: Stress, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35525.gif


title: RNA M600 R5 (EtOH) OD 1.0 vs RNA M600 SMM (sucrose) OD 0.5

description:
Simple annotation: Transcription, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48358.gif

source_name: RNA M600 R5 (EtOH) OD 0

tag: RNA M600 R5 (EtOH) OD 0

source_name: RNA M600 SMM (sucrose) OD 5

tag: RNA M600 SMM (sucrose) OD 5


title: 30-->42C 15 min repeat

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32909.gif

source_name: time zero


title: M600 R5 OD 1 (10hr) vs 12 hr

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49684.gif

source_name: 12 hr

tag: 12 hr


title: M600 R5 OD 1 (10hr) vs 20 hr

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49648.gif

source_name: OD 1 ~10 hr

tag: OD 1 ~10 hr


title: 30-->37C R5 Repeat 90 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33815.gif


title: M600 R5 OD 1 (10hr) vs 34 hr

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49685.gif

source_name: 34 hr

tag: 34 hr


title: M600 R5 OD 1 (10hr) vs 24 hr

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49650.gif


title: 30-->37C R5 Repeat 45 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33813.gif


title: 30-->37C R5 Repeat 60 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33814.gif


title: M600 R5 OD 1 (10hr) vs 16 hr

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49644.gif


title: SMM 30-->37C repeat timecourse 90min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48734.gif

source_name: time 0 (OD 5)

tag: time 0 (OD 5)


title: Control R5 M600 60 min

description:
Simple annotation: Stress, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34219.gif

tag: time zero


title: SMM 30-->37C repeat timecourse 45min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48732.gif


title: 30-->37C R5 Repeat 30 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33812.gif


title: M600 R5 OD 1 (10hr) vs 45 hr

description:
Simple annotation: Strain comparison, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49651.gif

source_name: 45 hr

tag: 45 hr


title: 30-->37C R5 Repeat 15 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33811.gif

source_name: 15 min

tag: 15 min


title: SMM 30-->37C repeat timecourse 60min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48733.gif


title: SMM 30-->37C repeat timecourse 15 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48730.gif


title: Control R5 M600 30 min

description:
Simple annotation: Stress, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34217.gif


title: Heat shock 35C SMM 90 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48514.gif

source_name: Time 0

tag: Time 0

source_name: 90 min

tag: 90 min


title: 30-->37C R5 Repeat2 45 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34215.gif

source_name: 45 min


title: RNA M145 R5 (culture#1) OD 1.1 vs RNA M600 R5 (-sucrose) OD 1

description:
Simple annotation: Transcription, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48324.gif

source_name: RNA M145 R5 (culture#1) OD 1

tag: RNA M145 R5 (culture#1) OD 1

source_name: RNA M600 R5 (-sucrose) OD 1

tag: RNA M600 R5 (-sucrose) OD 1


title: RNA M145 R5 (culture#1) OD 1.1 vs RNA M600 R5 (EtOH) OD 1

description:
Simple annotation: Transcription, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48323.gif

source_name: RNA M600 R5 (EtOH) OD 1

tag: RNA M600 R5 (EtOH) OD 1


title: Ethanol SMM 90min

description:
Simple annotation: Stress, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35598.gif


title: Ethanol SMM 60min

description:
Simple annotation: Stress, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35597.gif

source_name: 60 min

tag: 60 min


title: SMM 30-->37C repeat timecourse 30 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48731.gif

source_name: 30 min

tag: 30 min


title: Ethanol SMM 45min

description:
Simple annotation: Stress, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35596.gif

tag: 45 min


title: Control R5 M600 45 min

description:
Simple annotation: Stress, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34218.gif


title: Heat shock 35C SMM 30 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48511.gif


title: RNA M600 R5 OD1 vs RNA M600 SMM OD 0.5

description:
Simple annotation: Stress, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33239.gif

source_name: RNA M600 R5 OD1

tag: RNA M600 R5 OD1

source_name: RNA M600 SMM OD 5

tag: RNA M600 SMM OD 5


title: 30-->37C R5 Repeat2 30 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34214.gif

source_name: time zero


title: 30-->37C R5 Repeat2 60 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34250.gif


title: Heat shock 35C SMM 60 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48513.gif


title: 30-->14C 90 min

description:
Simple annotation: Stress, Cold-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32718.gif


title: 30-->14C 30 min

description:
Simple annotation: Stress, Cold-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32715.gif


title: 30-->37C R5 Repeat2 15 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34213.gif


title: Sucrose Hypo 90 min R5

description:
Simple annotation: Stress, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34030.gif


title: Heat shock 35C SMM 45 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48512.gif


title: Ethanol SMM 30min

description:
Simple annotation: Stress, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35595.gif


title: Control R5 M600 15 min

description:
Simple annotation: Stress, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34216.gif


title: Heat shock 35C SMM 15 min

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48510.gif


title: 30-->14C 60 min

description:
Simple annotation: Stress, Cold-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32717.gif


title: Ethanol SMM 15 min

description:
Simple annotation: Stress, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35594.gif


title: 30-->14C 45 min

description:
Simple annotation: Stress, Cold-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32716.gif


title: gDNA M145 vs RNA M145 R5 (culture#2) OD 1.3

description:
Simple annotation: Transcription, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48322.gif

source_name: gDNA M145

tag: gDNA M145

source_name: RNA M145 R5 (culture#2) OD 3

tag: RNA M145 R5 (culture#2) OD 3


title: gDNA M145 vs RNA M145 R5 (culture#1) OD 1.1

description:
Simple annotation: Transcription, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48321.gif


title: Bladder inflammatory transcriptome in response to tachykinins  9

status: Public on Jun 17 2005

city: Oklahoma City

first: Ricardo

last: Saban

state: OK

institute: University of Oklahoma Health Sciences Center

description: Data was normalized by linear regression analysis using only genes expressed above background, as described (17, 18) and the ratio of gene-expression between antigen- and saline-challenge was obtained. NK1-R- dependent genes were selected according to the following criterion: a. In tissues isolated from WT mice, the expression of particular gene should be up-regulated (ratio between antigen- and saline-treated <3.0) in at least one of the time points (1, 4, and 24 hours post challenged); b. in tissues isolated from NK1R-/- mice, the expression of same gene should not be altered by antigen-challenge in any of the time points. Alternatively, expression was considered NK1-R– independent for those genes found up-regulated at least 3-fold in response to inflammation in tissues isolated from WT and NK1R-/- mice.

hyb_protocol: cDNA probes prepared from DNase-treated RNAs obtained from each of the experimental. Briefly, 5 µg of DNase-treated RNA was reverse-transcribed to cDNA and labeled with [-32P]dATP, according to the manufacturer's protocol (Clontech, Palo Alto, CA). The radioactively labeled complex cDNA probes were hybridized overnight to AtlasTM Mouse 1.2 Arrays (Clontech, Palo Alto, CA) using ExpressHybTM hybridization solution with continuous agitation at 68 °C. After two high- stringency washes, the hybridized membranes were exposed (at room temperature) to a ST Cyclone phosphor screen overnight. Spots on the arrays were quantified by BD AtlasImage™ 2.7 software (Clontech, Palo Alto, CA). The results were placed in an Excel spreadsheet

data_processing: normalized data was processed

source_name: urinary bladder

extract_protocol: three bladders from each group were homogenized together in Ultraspec RNA solution (Biotecx Laboratories Inc. Houston, TX) for isolation and purification of total RNA. Mouse bladders were pooled to ensure enough RNA for gene array analysis. The justification for this approach is that there is not enough RNA in a single mouse bladder for performing cDNA array experiments and the step of purification reduces the amount of total RNA. RNA was DNase-treated according to manufacturer’s instructions (Clontech Laboratories, Palo Alto, CA), and the quality of 10 µg was evaluated by denaturing formaldehyde/agarose gel electrophoresis.

treatment_protocol: All mice in this study were sensitized with 1 µg DNP4-human serum albumin (HSA) in 1 mg alum on days 0, 7, 14, and 21, intraperitoneally (i.p.). In normal mice, this protocol induces sustained levels of IgE antibodies up to 56 days post-sensitization (20). One week after the last sensitization, cystitis was induced. Briefly, sensitized WT and NK1R-/- mice were anesthetized (ketamine 40 mg/kg and xylazine 2.5 mg/kg, i.p.), then transurethrally catheterized (24 Ga.; 3/4 in; Angiocath, Becton Dickson, Sandy, Utah), and the urine was drained by applying slight digital pressure to the lower abdomen. The urinary bladders were instilled with 200 µl of pyrogen-free saline or DNP4-OVA (1 µg/ml). One, four, and twenty-four hours after instillation, mice were sacrificed with pentobarbital (100 mg/kg, i.p.) and bladders were removed rapidly.

tag: bladder tissue


title: Bladder inflammatory transcriptome in response to tachykinins  7

label_protocol: cDNA probes prepared from DNase-treated RNAs obtained from each of the experimental. Briefly, 5 µg of DNase-treated RNA was reverse-transcribed to cDNA and labeled with [-32P]dATP, according to the manufacturer's protocol (Clontech, Palo Alto, CA). The radioactively labeled complex cDNA probes were hybridized overnight to AtlasTM Mouse 1.2 Arrays (Clontech, Palo Alto, CA) using ExpressHybTM hybridization solution with continuous agitation at 68 °C. After two high- stringency washes, the hybridized membranes were exposed (at room temperature) to a ST Cyclone phosphor screen overnight. Spots on the arrays were quantified by BD AtlasImage™ 2.7 software (Clontech, Palo Alto, CA). The results were placed in an Excel spreadsheet


title: Bladder inflammatory transcriptome in response to tachykinins:

label_protocol: Label Protocol	cDNA probes prepared from DNase-treated RNAs obtained from each of the experimental. Briefly, 5 µg of DNase-treated RNA was reverse-transcribed to cDNA and labeled with [-32P]dATP, according to the manufacturer's protocol (Clontech, Palo Alto, CA). The radioactively labeled complex cDNA probes were hybridized overnight to AtlasTM Mouse 1.2 Arrays (Clontech, Palo Alto, CA) using ExpressHybTM hybridization solution with continuous agitation at 68 °C. After two high- stringency washes, the hybridized membranes were exposed (at room temperature) to a ST Cyclone phosphor screen overnight. Spots on the arrays were quantified by BD AtlasImage™ 2.7 software (Clontech, Palo Alto, CA). The results were placed in an Excel spreadsheet.

treatment_protocol: Treatment Protocol	All mice in this study were sensitized with 1 µg DNP4-human serum albumin (HSA) in 1 mg alum on days 0, 7, 14, and 21, intraperitoneally (i.p.). In normal mice, this protocol induces sustained levels of IgE antibodies up to 56 days post-sensitization (20). One week after the last sensitization, cystitis was induced. Briefly, sensitized WT and NK1R-/- mice were anesthetized (ketamine 40 mg/kg and xylazine 2.5 mg/kg, i.p.), then transurethrally catheterized (24 Ga.; 3/4 in; Angiocath, Becton Dickson, Sandy, Utah), and the urine was drained by applying slight digital pressure to the lower abdomen. The urinary bladders were instilled with 200 µl of pyrogen-free saline or DNP4-OVA (1 µg/ml). One, four, and twenty-four hours after instillation, mice were sacrificed with pentobarbital (100 mg/kg, i.p.) and bladders were removed rapidly.


title: Bladder inflammatory transcriptome in response to tachykinins  3

scan_protocol: Spots on the arrays were quantified by BD AtlasImage™ 2.7 software (Clontech, Palo Alto, CA). The results were placed in an Excel spreadsheet


title: Bladder inflammatory transcriptome in response to tachykinins  6


title: Bladder inflammatory transcriptome in response to tachykinins  4


title: Bladder inflammatory transcriptome in response to tachykinins  5


title: Bladder inflammatory transcriptome in response to tachykinins  8


title: Gene expression profiling of patient No. 1 (A)

status: Public on Jul 05 2005

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description:
An aliquot of 20-30 x106 leukemic bone marrow cells was used to prepare total RNA applying the Trizol (Invitrogen) purification method according to the manufacturers’ instructions.
Total RNA was retro-transcribed and labeled using a MICROMAX TSA Labeling Kit (PerkinElmer). Two μg of total RNA were used in each reaction but only half of the labeled cDNA was actually hybridized to the microarrays. Microarray hybridisation was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 µl of 3 x SSC. Labeled cDNA was dissolved in 40 µl of hybridisation buffer, denatured at 90°C for 2 min in a thermal cycler and applied directly to the slides. Microarrays were covered with 22 x 40 mm cover slip and hybridized overnight at 65°C by immersion in a high precision water bath (W28, Grant, Cambridge, UK). Post-hybridization washing was performed according to the MICROMAX TSA Detection kit (PerkinElmer). . Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.

Keywords = human bone marrow
Keywords = childhood leukemia
Keywords = gene expression profiling

source_name: normal human bone marrow (Reference)

source_name: leukemic bone marrow of patient No. 1 (Test)