title: 67:21 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10880.gif

source_name: 2 ug 67:21 genomic DNA

tag: 2 ug 67:21 genomic DNA


title: wnt3a vs control; on human embryonal CA (svm034)

status: Public on Sep 08 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: wnt, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3592.gif

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

molecule: total RNA

organism: Homo sapiens

source_name: control

tag: control


title: CA50 vs Tigr/Astra Reference 2

status: Public on Sep 09 2005

type: genomic

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10864.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: genomic DNA

organism: Helicobacter pylori

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

source_name: 2 ug CA50 genomic DNA

tag: 2 ug CA50 genomic DNA


title: CA55 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10872.gif

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

source_name: 2 ug CA55 genomic DNA

tag: 2 ug CA55 genomic DNA


title: wnt3a vs control, on HTC, 3 hr (svl015)

description:
Simple annotation: wnt, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/6959.gif


title: CA8 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10871.gif

source_name: 2 ug CA8 genomic DNA

tag: 2 ug CA8 genomic DNA


title: wnt3A vs control; 4 hr

description:
Simple annotation: wnt, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/8041.gif

source_name: wnt3A; 4 hr

tag: wnt3A; 4 hr

source_name: control; 4 hr

tag: control; 4 hr


title: wnt3A

description:
Simple annotation: wnt, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4599.gif


title: Hp1 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10881.gif

source_name: 2 ug Hp1 genomic DNA

tag: 2 ug Hp1 genomic DNA


title: control 61:4 genomic DNA vs. Tigr/Astra ref

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10211.gif

source_name: 1 ug 26695 genomic DNA + 1ug J99 genomic DNA

source_name: 2 ug control 61:4 genomic DNA

tag: 2 ug control 61:4 genomic DNA


title: wnt3A (10X) vs control; 4 hr

description:
Simple annotation: wnt, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/8045.gif

source_name: wnt3A (10X); 4 hr

tag: wnt3A (10X); 4 hr


title: B7

status: Public on Aug 31 2005

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29776.gif

organism: Mus musculus

source_name: pooled aged matched control samples

tag: pooled aged matched control samples

source_name: gastric biopsy JO11 B7

tag: gastric biopsy JO11 B7


title: B8

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29778.gif

source_name: gastric biopsy JO11 B8

tag: gastric biopsy JO11 B8


title: D7

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29774.gif

source_name: gastric biopsy JO11 D7

tag: gastric biopsy JO11 D7


title: B3

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29621.gif

source_name: gastric biopsy JO11 B3

tag: gastric biopsy JO11 B3


title: C3

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29638.gif

source_name: gastric biopsy JO11 C3

tag: gastric biopsy JO11 C3


title: D8

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29775.gif

source_name: gastric biopsy JO11 D8

tag: gastric biopsy JO11 D8


title: C6

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29647.gif

source_name: gastric biopsy JO11 C6

tag: gastric biopsy JO11 C6


title: A9

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29622.gif

source_name: gastric biopsy JO11 A9

tag: gastric biopsy JO11 A9


title: B2

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29670.gif

source_name: gastric biopsy JO11 B2

tag: gastric biopsy JO11 B2


title: C7

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29648.gif

source_name: gastric biopsy JO11 C7

tag: gastric biopsy JO11 C7


title: CA52 vs Tigr/Astra Reference 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10870.gif

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

source_name: 2 ug CA52 genomic DNA

tag: 2 ug CA52 genomic DNA


title: C2

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29637.gif

source_name: gastric biopsy JO11 C2

tag: gastric biopsy JO11 C2


title: D5

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29645.gif

source_name: gastric biopsy JO11 D5

tag: gastric biopsy JO11 D5


title: B4

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29629.gif

source_name: gastric biopsy JO11 B4

tag: gastric biopsy JO11 B4


title: WT 24h micro

status: Public on Aug 27 2005

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32170.gif

organism: Campylobacter jejuni

source_name: 2ug RNA from sample pool

tag: 2ug RNA from sample pool

source_name: 2ug RNA from WT 24h micro

tag: 2ug RNA from WT 24h micro


title: B6

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29635.gif

source_name: pooled aged matched control samples

tag: pooled aged matched control samples

source_name: gastric biopsy JO11 B6

tag: gastric biopsy JO11 B6


title: D4

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29644.gif

source_name: gastric biopsy JO11 D4

tag: gastric biopsy JO11 D4


title: B1

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29619.gif

source_name: gastric biopsy JO11 B1

tag: gastric biopsy JO11 B1


title: ChX vs CHO

description:
Simple annotation: Somatic cell hybrid, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/11971.gif

source_name: CHO

tag: CHO

source_name: ChX

tag: ChX


title: SSA 24h micro

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32528.gif

source_name: "2ug RNA from sample pool (WT, spoT, SSA)"

source_name: 2ug RNA from SSA 24h micro

tag: 2ug RNA from SSA 24h micro


title: C1

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29636.gif

source_name: gastric biopsy JO11 C1

tag: gastric biopsy JO11 C1


title: A7

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29617.gif

source_name: gastric biopsy JO11 A7

tag: gastric biopsy JO11 A7


title: spoT 30' micro

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32161.gif

source_name: 2ug RNA from spoT 30' micro

tag: 2ug RNA from spoT 30' micro


title: A11

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29626.gif

source_name: gastric biopsy JO11 A11

tag: gastric biopsy JO11 A11


title: SSA 6h micro

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32527.gif

tag: "2ug RNA from sample pool (WT, spoT, SSA)"

source_name: 2ug RNA from SSA 6h micro

tag: 2ug RNA from SSA 6h micro


title: WT 30' micro

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32160.gif

source_name: 2ug RNA from WT 30' micro

tag: 2ug RNA from WT 30' micro


title: spoT 6h micro

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32169.gif

source_name: 2ug RNA from spoT 6h micro

tag: 2ug RNA from spoT 6h micro


title: WT 6h micro

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32168.gif

source_name: 2ug RNA from sample pool

tag: 2ug RNA from sample pool

source_name: 2ug RNA from WT 6h micro

tag: 2ug RNA from WT 6h micro


title: SSA 30' micro

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32523.gif

source_name: 2ug RNA from SSA 30' micro

tag: 2ug RNA from SSA 30' micro


title: D6

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29646.gif

source_name: pooled aged matched control samples

tag: pooled aged matched control samples

source_name: gastric biopsy JO11 D6

tag: gastric biopsy JO11 D6


title: A8

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29618.gif

source_name: gastric biopsy JO11 A8

tag: gastric biopsy JO11 A8


title: C5

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29640.gif

source_name: gastric biopsy JO11 C5

tag: gastric biopsy JO11 C5


title: A10

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29624.gif

source_name: gastric biopsy JO11 A10

tag: gastric biopsy JO11 A10


title: B5

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29633.gif

source_name: gastric biopsy JO11 B5

tag: gastric biopsy JO11 B5


title: A6

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29616.gif

source_name: gastric biopsy JO11 A6

tag: gastric biopsy JO11 A6


title: D2

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29642.gif

source_name: gastric biopsy JO11 D2

tag: gastric biopsy JO11 D2


title: D3

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29643.gif

source_name: gastric biopsy JO11 D3

tag: gastric biopsy JO11 D3


title: WT 2h micro

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32164.gif

source_name: 2ug RNA from WT 2h micro

tag: 2ug RNA from WT 2h micro


title: spoT 2h micro

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32165.gif

source_name: 2ug RNA from spoT 2h micro

tag: 2ug RNA from spoT 2h micro


title: D1

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29641.gif

source_name: gastric biopsy JO11 D1

tag: gastric biopsy JO11 D1


title: HPRT2 vs CHO

description:
Simple annotation: Somatic cell hybrid, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/11982.gif

source_name: CHO

tag: CHO


title: spoT 24h micro

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32171.gif

source_name: 2ug RNA from spoT 24h micro

tag: 2ug RNA from spoT 24h micro


title: C4

description:
Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29639.gif

source_name: gastric biopsy JO11 C4

tag: gastric biopsy JO11 C4


title: SSA 2h micro

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32525.gif

source_name: "2ug RNA from sample pool (WT, spoT, SSA)"

source_name: 2ug RNA from SSA 2h micro

tag: 2ug RNA from SSA 2h micro


title: JVM-HH

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Prolymphocytic Leukemia (PLL)
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2874.gif

source_name: Lymphopool

tag: Lymphopool

source_name: JVM-HH

tag: JVM-HH


title: CLL-52

description:
Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2838.gif


title: CLL-58

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2648.gif


title: CLL-61

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2656.gif


title: CLL-15

description:
Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2985.gif


title: CLL-70;Lymph node

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2617.gif

source_name: CLL-70;Lymph node

tag: CLL-70;Lymph node


title: CLL-41

description:
Simple annotation: Chronic Lymphocytic Leukemia, ARA-G in vivo chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2765.gif


title: CLL-65

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2659.gif


title: CLL-60

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2653.gif


title: CLL-59

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2650.gif


title: CLL-39

description:
Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2975.gif


title: CLL-57

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2646.gif


title: CLL-49

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2642.gif


title: CLL-47

description:
Simple annotation: Chronic Lymphocytic Leukemia, ARA-G in vivo chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2823.gif


title: CLL-51

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2644.gif


title: CLL-62

description:
Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/3087.gif


title: CLL-48

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2640.gif


title: CLL-21

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2674.gif


title: ovca14-LMP

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31228.gif

source_name: UHR

tag: UHR

source_name: ovca14-LMP Total RNA

tag: ovca14-LMP Total RNA


title: ovca44-LMP

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31236.gif

source_name: ovca44-LMP Total RNA

tag: ovca44-LMP Total RNA


title: CLL-45

description:
Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2856.gif


title: CLL-25

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2675.gif


title: CLL-22

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2671.gif


title: CLL-16

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2673.gif


title: CLL-46

description:
Simple annotation: Chronic Lymphocytic Leukemia, ARA-G in vivo chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2701.gif


title: CLL-17

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2670.gif


title: ovca41-LMP

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31216.gif

source_name: ovca41-LMP Total RNA

tag: ovca41-LMP Total RNA


title: CLL-29

description:
Simple annotation: Chronic Lymphocytic Leukemia, ARA-G in vivo chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/3031.gif


title: CLL-24

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2672.gif


title: CLL-19

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2669.gif


title: ovca23-Gr2

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31207.gif

source_name: ovca23-Gr2 Total RNA

tag: ovca23-Gr2 Total RNA


title: ovca32-Gr3

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31215.gif

source_name: ovca32-Gr3 Total RNA

tag: ovca32-Gr3 Total RNA


title: ovca34-Gr3

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31945.gif

source_name: ovca34-Gr3 Total RNA

tag: ovca34-Gr3 Total RNA


title: ovca27-LMP

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31211.gif

source_name: ovca27-LMP Total RNA

tag: ovca27-LMP Total RNA


title: CLL-53

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2668.gif


title: CLL-55

description:
Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2772.gif


title: CLL-69

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2666.gif


title: CLL-10

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2667.gif


title: CLL-67

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2664.gif


title: CLL-50

description:
Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2842.gif


title: CLL-68

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2665.gif


title: ovca19-LMP

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31204.gif

source_name: ovca19-LMP Total RNA

tag: ovca19-LMP Total RNA


title: CLL-66;SL106

description:
Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2662.gif


title: ovca30-Gr2

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31212.gif

source_name: ovca30-Gr2 Total RNA

tag: ovca30-Gr2 Total RNA


title: ovca43-Gr3

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31952.gif

source_name: ovca43-Gr3 Total RNA

tag: ovca43-Gr3 Total RNA


title: ovca45-LMP

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31955.gif

source_name: ovca45-LMP Total RNA

tag: ovca45-LMP Total RNA


title: ovca11-Gr2

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31202.gif

source_name: ovca11-Gr2 Total RNA

tag: ovca11-Gr2 Total RNA


title: ovca8-Gr2

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31222.gif

source_name: ovca8-Gr2 Total RNA

tag: ovca8-Gr2 Total RNA


title: batch 02X25 4

status: Public on Aug 26 2005

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34360.gif

organism: Saccharomyces cerevisiae

tag: "Chemostat

source_name: "batch, hour 9.5"

tag: "batch, hour 9.5"


title: batch 02X25 3

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34359.gif

source_name: "batch, hour 9"

tag: "batch, hour 9"


title: batch 02X25 5

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34362.gif

source_name: "batch, hour 10"

tag: "batch, hour 10"


title: batch 02X25 1

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34357.gif

source_name: "batch, hour 6"

tag: "batch, hour 6"


title: ovca9-Gr2

description:
Simple annotation: Primary tumor, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31942.gif

source_name: UHR

tag: UHR

source_name: ovca9-Gr2 Total RNA

tag: ovca9-Gr2 Total RNA


title: ovca2-LMP

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31941.gif

source_name: ovca2-LMP Total RNA

tag: ovca2-LMP Total RNA


title: ovca38-Gr2

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31950.gif

source_name: ovca38-Gr2 Total RNA

tag: ovca38-Gr2 Total RNA


title: ovca22-LMP

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31205.gif

source_name: ovca22-LMP Total RNA

tag: ovca22-LMP Total RNA


title: batch 02X25 6

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34365.gif

source_name: "batch, hour 10.5"

tag: "batch, hour 10.5"


title: ovca10-LMP

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31194.gif

source_name: ovca10-LMP Total RNA

tag: ovca10-LMP Total RNA


title: ovca7-Gr3

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31219.gif

source_name: ovca7-Gr3 Total RNA

tag: ovca7-Gr3 Total RNA


title: 03II01 batch p12

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38156.gif

tag: "DBY10085 Chemostat

source_name: DBY10085 Batch timepoint 12

tag: DBY10085 Batch timepoint 12


title: batch 02X25 2

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34358.gif

source_name: "batch, hour 8"

tag: "batch, hour 8"


title: 03II01 batch p3

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38147.gif

source_name: DBY10085 Batch timepoint 3

tag: DBY10085 Batch timepoint 3


title: ovca4-Gr1

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31186.gif

source_name: ovca4-Gr1Total RNA

tag: ovca4-Gr1Total RNA


title: ovca1-Gr3

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31191.gif

source_name: ovca1-Gr3 Total RNA

tag: ovca1-Gr3 Total RNA


title: ovca5-LMP

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31184.gif

source_name: ovca5-LMP Total RNA

tag: ovca5-LMP Total RNA


title: 03II01 batch p5

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38149.gif

source_name: DBY10085 Batch timepoint 5

tag: DBY10085 Batch timepoint 5


title: 03II01 batch p11

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38155.gif

source_name: DBY10085 Batch timepoint 11

tag: DBY10085 Batch timepoint 11


title: 03II01 batch p9

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38153.gif

source_name: DBY10085 Batch timepoint 9

tag: DBY10085 Batch timepoint 9


title: Low-D chemostat vs. High-D chemostat

description:
Simple annotation: Chemostat, Dilution Rate
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45181.gif

source_name: Reference: D=0.25

tag: Reference


title: ovca29-Gr3

description:
Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31951.gif

source_name: UHR

tag: UHR

source_name: ovca29-Gr3 Total RNA

tag: ovca29-Gr3 Total RNA


title: 03II01 batch p10

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38154.gif

source_name: DBY10085 Batch timepoint 10

tag: DBY10085 Batch timepoint 10


title: B7, nonhost/untreated (18 hpi), exp5

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27385.gif

organism: Arabidopsis thaliana

source_name: untreated

tag: untreated

source_name: nonhost

tag: nonhost


title: 03II01 batch p7

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38151.gif

source_name: DBY10085 Batch timepoint 7

tag: DBY10085 Batch timepoint 7


title: 03II01 batch p2

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38146.gif

tag: "DBY10085 Chemostat

source_name: DBY10085 Batch timepoint 2

tag: DBY10085 Batch timepoint 2


title: 03II01 batch p4

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38148.gif

source_name: DBY10085 Batch timepoint 4

tag: DBY10085 Batch timepoint 4


title: 03II01 batch p8

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38152.gif

source_name: DBY10085 Batch timepoint 8

tag: DBY10085 Batch timepoint 8


title: 03II01 batch p6

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38150.gif

source_name: DBY10085 Batch timepoint 6

tag: DBY10085 Batch timepoint 6


title: A4, host/untreated (8 hpi), exp6

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26648.gif

source_name: host

tag: host


title: A11, host/untreated (24 hpi), exp 5

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27638.gif


title: B3, nonhost/untreated (8 hpi), exp 5

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27689.gif


title: B11, nonhost/untreated (24 hpi), exp5

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27272.gif


title: A1, host/untreated (8 hpi), exp1

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21091.gif


title: B1, nonhost/untreated (8 hpi), exp1

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21355.gif


title: A2, host/untreated (8 hpi), exp2

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21092.gif


title: B9, nonhost/untreated (24 hpi), exp1

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22034.gif


title: B8, nonhost/untreated (18 hpi), exp6

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26611.gif


title: A7, host/untreated (18 hpi), exp5

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27384.gif


title: B12, nonhost/untreated (24 hpi), exp6

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26885.gif


title: batch 02X25 7

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34368.gif

tag: "Chemostat

source_name: "batch, hour 11"

tag: "batch, hour 11"


title: 300p-16 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24529.gif


title: 300p-14 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24527.gif


title: A6, host/untreated (18 hpi), exp2

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20783.gif


title: B10, nonhost/untreated (24 hpi), exp2

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-11/22202.gif


title: A10, host/untreated (24 hpi), exp2

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20788.gif


title: 300p-13 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24526.gif


title: 300p-15 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24528.gif


title: Treated 1 Cy5-labeled total RNA on Array 3

city: Baltimore

first: Djikolngar

last: Maouyo

state: MD

institute: University of Maryland Baltimore

description: High quality spotted cDNA on glass slide microarrays were purchased from the Microarray Centre of the University Health Network (Toronto, Canada). These arrays contained PCR-generated cDNA inserts of all 15,264 sequence-verified mouse ESTs, from the National Institute of Aging collection. Duplicate 100-mm diameter cDNA spots are represented on GAPS II slides (Corning, Inc.). Spot cDNA identity is tracked by composed identifiers including clone identifier, description, and Unigene, and catalogued as “M15Kv1”.

hyb_protocol: The labeled cDNAs from the control and test samples were mixed and hybridized with the mouse cDNA arrays in humidified hybridization chambers at 60°C for 18 hours. After 3-step wash, cDNA arrays were then hybridized with Cy5-coupled dendrimers at 60°C for 4 hours. http://www.genisphere.com/array_detection_home.html.

scan_protocol: Slides were read using a laser confocal scanner, the GSI Lumonics ScanArray 5000 imaging system, at 10-µm resolution set up for excitation/emission at 649/670 nm, and for acquisition of Cy3-labeled spots respectively.

data_processing: Prior to data analysis, data were normalized so that total intensity of both channels was equal using an algorithm provided by TM4-MIDAS (www.tm4.org). Relative transcript abundance was deduced from the ratio of the background-subtracted and normalized Cy5/Cy3 fluorescence intensities at each target, the so-called expression ratio. Significantly up-regulated or down-regulated genes on individual arrays were identified from frequency-log expression ratio histogram as data points that were at least ± 1.5 X standard deviation from the mean expression ratio.

source_name: Cortical collecting duct M-1 cells

label_protocol: Five-microgram total RNA was reverse-transcribed using oligo-dT flanked at 5’ end with capture sequences specific to fluorescent Cy5-coupled dendrimer complexes.

growth_protocol: M-1 cells derived from mouse cortical collecting duct cells (57) were grown at 37C in 5% CO2 in complete PC-1 medium (BioWhittaker, Maryland) supplemented with 100 U/ml penicillin/100 mg/ml streptomycin and 2 mM glutamine. After cells reached confluence, the PC-1 medium was replaced with a medium nominally free of steroid hormones (DMEM/F12 medium containing 2 mM glutamine, 100 U/ml penicillin G/100 mg/ml streptomycin, 10% charcoal and dextran-treated fetal bovine serum) for 24 to 36 hours.

extract_protocol: RNA samples from dexamethasone-treated and control cells were extracted with Trizol reagent, and DNA-decontaminated using DNA-free kit, commercially available (Ambion, Austin, TX).

treatment_protocol: Cells were then treated with 100 nM hydrosoluble dexamethasone for 3 hours at 37 degree Celcius with 5% CO2.

tag: Mouse cortical collecting duct cells;

tag: M-1 Cell line;

tag: Passage number

tag: Confluent and polarized cells.


title: Treated 3 Cy5-labeled total RNA on Array 5

scan_protocol: Slides were read using a laser confocal scanner, the GSI Lumonics ScanArray 5000 imaging system, at 10-µm resolution set up for excitation/emission at 649/670 nm, and for acquisition of Cy5-labeled spots respectively.

label_protocol: Five-microgram total RNA was reverse-transcribed using oligo-dT flanked at 5’ end with capture sequences specific to fluorescent Cy3-coupled dendrimer complexes.

extract_protocol: RNA samples from dexamethasone-treated were extracted with Trizol reagent, and DNA-decontaminated using DNA-free kit, commercially available (Ambion, Austin, TX).

treatment_protocol: Cells were then treated with 100nM dexamethasone for 3 hours at 37 degree Celcius with 5% CO2.


title: Control 4 Cy3-labeled total RNA on Array 4

scan_protocol: Slides were read using a laser confocal scanner, the GSI Lumonics ScanArray 5000 imaging system, at 10-µm resolution set up for excitation/emission at 543/570 nm, and for acquisition of Cy3-labeled spots respectively.

tag: Confluent and polarized cells


title: 300p-12 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24525.gif


title: 300p-20 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23870.gif


title: A3, host/untreated (8 hpi), exp5

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27687.gif


title: Control 3 Cy3-labeled total RNA on Array 3


title: 300p-8 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24521.gif


title: B2, nonhost/untreated (8 hpi), exp2

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20767.gif


title: Control 5 Cy3-labeled total RNA on Array 5

treatment_protocol: Cells were then treated with steroid-free medium for 3 hours at 37 degree Celcius with 5% CO2.


title: Treated 2 Cy5-labeled total RNA on Array 4

tag: Confluent and polarized cell;


title: 300p-10 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24523.gif


title: 300p-11 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24524.gif


title: Control 2 Cy5-labeled total RNA

tag: Mouse cortical collecting duct cells

tag: M-1 Cell line


title: Control 2 Cy3-labeled total RNA


title: Control 1 Cy3-labeled total RNA

hyb_protocol: The labeled cDNAs from the control and test samples were mixed and hybridized with the mouse cDNA arrays in humidified hybridization chambers at 60°C for 18 hours. After 3-step wash, cDNA arrays were then hybridized with Cy3-coupled dendrimers for 4 hours. http://www.genisphere.com/array_detection_home.html

scan_protocol: Slides were read using a laser confocal scanner, the GSI Lumonics ScanArray 5000 imaging system, at 10-µm resolution set up for excitation/emission at 543/570 nm, and for acquisition of Cy3-labeled spots.

source_name: Mouse cortical collecting duct M-1 cells

label_protocol: 5-microgram total RNA was reverse-transcribed using oligo-dT flanked at 5’ end with capture sequences specific to fluorescent Cy3-coupled dendrimer complexes.

treatment_protocol: Cells were then treated with steroid-free medium for 3 hours at 37°C with 5% CO2.


title: 300p-9 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24522.gif


title: 300p-7 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24520.gif


title: 300p-10 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23611.gif


title: 300p-9 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23610.gif


title: 300p-17 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23867.gif


title: 300p-18r 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24534.gif


title: 300p-19 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23869.gif


title: 300p-15 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23865.gif


title: 300p-20 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24533.gif


title: 300p-14 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23864.gif


title: 300p-18 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23868.gif


title: 300p-11 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23861.gif


title: 300p-13 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23863.gif


title: 300p-16 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23866.gif


title: 300p-1 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24514.gif


title: 300p-6 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23607.gif


title: 300p-8 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23609.gif


title: 300p-7 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23608.gif


title: 300p-4 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23605.gif


title: 300p-19r 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24535.gif


title: 300p-4 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24517.gif


title: 300p-18 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24531.gif


title: 300p-2 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24515.gif


title: 300p-5 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24518.gif


title: 300p-5 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23606.gif


title: 300p-17 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24530.gif


title: 300p-6 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24519.gif


title: 300p-3 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23604.gif


title: 300p-3 2C-N vs 2C-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24516.gif


title: 300p-1 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23602.gif


title: Strain H37Rv, 2-3, MM026

type: mixed

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14049.gif

organism: Mycobacterium tuberculosis

source_name: H37Rv genomic DNA control

tag: H37Rv genomic DNA control

source_name: H37Rv RNA, 23

tag: H37Rv RNA, 23


title: Strain 9700665, 16-2, MM321

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15478.gif


title: Strain 9700665, 16-3, MM322

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs//15479.gif


title: Strain 1254, 1-4, MM077

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15279.gif


title: Strain M3061a, 5-2, MM079

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15587.gif


title: Strain H37Ra, 3-4, MM035

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14040.gif

source_name: H37Ra RNA, 3-4

tag: H37Ra RNA, 3-4


title: Strain 1843, 14-4, MM315

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15472.gif


title: Strain M3061a, 5-1, MM097

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15586.gif


title: Strain CDC1551, 4-1, MM043

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15569.gif


title: Strain 1006, 15-2, MM329

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15474.gif


title: 03II01 batch p1

description:
Simple annotation: Starvation, Diauxic shift
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38145.gif

tag: "DBY10085 Chemostat

source_name: DBY10085 Batch timepoint 1

tag: DBY10085 Batch timepoint 1


title: Strain M3061a, 5-3, MM080

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15588.gif


title: Strain H37Rv, 2-1, MM024

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14047.gif

source_name: H37Rv RNA, 2-1

tag: H37Rv RNA, 2-1


title: B4, nonhost/untreated (8 hpi), exp6

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26880.gif

tag: untreated

tag: nonhost


title: Strain 9700665, 16-1, MM320

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15477.gif


title: Strain H37Rv, 2-2, MM025

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14048.gif

source_name: H37Rv RNA, 2-2

tag: H37Rv RNA, 2-2


title: Strain 3160, 13-2, MM071

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15365.gif


title: Strain 1006, 15-4, MM319

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15476.gif


title: Strain 3160, 13-3, MM023

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15366.gif


title: Strain 1843, 14-3, MM314

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15471.gif


title: Strain 9802826, 12-2, MM344

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16290.gif


title: Strain 1006, 15-3, MM318

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15475.gif


title: Strain H37Ra, 3-3, MM327

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14549.gif

source_name: H37Ra RNA, 3-3

tag: H37Ra RNA, 3-3


title: Strain 3160, 13-4, MM073

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs//15367.gif


title: Strain 1006, 15-1, MM328

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15473.gif


title: Strain 1843, 14-2, MM313

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15470.gif


title: Strain 3160, 13-1, MM070

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15364.gif


title: Strain 9802826, 12-4, MM311

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15363.gif


title: Strain 1254, 1-2, MM075

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15275.gif


title: Strain 9802826, 12-3, MM310

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15362.gif


title: Strain H37Ra, 3-2, MM029

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14038.gif

source_name: H37Ra RNA, 3-2

tag: H37Ra RNA, 3-2


title: GENOMIC DNA- E. histolytica- HK-9 (4ug) isolated from pellets grown here

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44369.gif

organism: Entamoeba histolytica

source_name: cy3 labeled pHOS reference

tag: cy3 labeled pHOS reference

source_name: cy5 labeled HK-9 genomic DNA

tag: cy5 labeled HK-9 genomic DNA


title: Strain 1254, 1-1, MM074

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15274.gif


title: GENOMIC DNA- E. dispar SAW760, 4ug genomic DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42456.gif

source_name: Cy3 labeled pHOS reference

tag: Cy3 labeled pHOS reference

source_name: Cy5 labeled Saw760 ED genomic DNA

tag: Cy5 labeled Saw760 ED genomic DNA


title: GENOMIC DNA-E. histolytica HK-9 hybed with 4ug genomic DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40779.gif

source_name: Cy5 labeled HK-9 genomic DNA

tag: Cy5 labeled HK-9 genomic DNA


title: GENOMIC DNA- E. dispar SAW1734 isolated here (7ug)

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44029.gif

source_name: Cy3 labeled pHOS reference DNA

tag: Cy3 labeled pHOS reference DNA

source_name: Cy5 labeled SAW1734 E. dispar genomic DNA (7ug)


title: Strain 9802826, 12-1, MM343

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16288.gif

tag: H37Rv genomic DNA control


title: Strain H37Rv, 2-4, MM027

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14050.gif

source_name: H37Rv RNA, 2-4

tag: H37Rv RNA, 2-4


title: GENOMIC DNA-E. histolytica (NIH200) with 8ug genomic DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42963.gif

source_name: Cy5 labeled NIH200 genomic DNA

tag: Cy5 labeled NIH200 genomic DNA


title: GENOMIC DNA- E. dispar- SAW760, 4ug genomic DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39359.gif

source_name: Cy3 labeled with pHOS reference DNA

tag: Cy3 labeled with pHOS reference DNA

source_name: Cy5 labeled with ED genomic DNA

tag: Cy5 labeled with ED genomic DNA


title: Strain CDC1551, 4-4, MM046

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15575.gif

source_name: H37Rv genomic DNA control


title: Strain 1843, 14-1, MM342

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16287.gif


title: GENOMIC DNA- E dispar SAW1734  hybed with 7ug genomic DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40780.gif

source_name: Cy5 labeled E.dispar SAW1734 genomic DNA


title: GENOMIC DNA- E. histolytica (HM1:IMSS)  sample 4, 4ug genomic DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/42455.gif

source_name: Cy5 labeled HM1 EH genomic DNA

tag: Cy5 labeled HM1 EH genomic DNA


title: GENOMIC DNA- E. dispar SAW760  4ug DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39358.gif


title: Strain H37Ra, 3-1, MM028

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14037.gif

source_name: H37Ra RNA, 3-1

tag: H37Ra RNA, 3-1


title: Strain M3061a, 5-4, MM081

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15590.gif


title: GENOMIC DNA - E.histolytica (HM1:IMSS) genomic DNA sample 6 (4ug)

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38116.gif

source_name: Cy3 labeled p-HOS reference

tag: Cy3 labeled p-HOS reference

source_name: Cy5 labeled Eh genomic DNA sample 6

tag: Cy5 labeled Eh genomic DNA sample 6


title: GENOMIC DNA-E. histolytica Rahman strain with 8ug genomic DNA

description:
Simple annotation: Strain comparison, Miscellaneous
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41187.gif

source_name: Cy5 labeled Rahman Genomic DNA

tag: Cy5 labeled Rahman Genomic DNA


title: GENOMIC DNA- E. histolytica (HM1:IMSS) 4ug genomic DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39357.gif

source_name: Cy5 labeled with EH genomic DNA

tag: Cy5 labeled with EH genomic DNA


title: GENOMIC DNA- E. histoytica strain HK-9 isolated here (4ug)

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44028.gif

source_name: Cy5 labeled HK-9 genomic DNA (4ug)

tag: Cy5 labeled HK-9 genomic DNA (4ug)


title: 300p-12 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23862.gif


title: GENOMIC DNA-E. dispar SAW1734 - 7ug genomic DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41188.gif

source_name: Cy5 labeled SAW1734 E.dispar Genomic DNA


title: Strain 9700665, 16-4, MM341

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16286.gif


title: Strain 9800608, 9-4, MM021

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15718.gif


title: Strain 1254, 1-3, MM076

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15277.gif


title: GENOMIC DNA- E. histolytica -NIH200- 8ug genomic DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40429.gif

source_name: Cy5 labeled genomic NIH200 genomic DNA

tag: Cy5 labeled genomic NIH200 genomic DNA


title: Strain CDC1551, 4-3, MM045

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15573.gif


title: Strain 9800608, 9-3, MM061

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15715.gif


title: 300p-2 2A-N vs 2A-S

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23603.gif


title: GENOMIC DNA-E. dispar SAW760 (4ug) DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38803.gif

source_name: Cy3 labeled pHOS reference

tag: Cy3 labeled pHOS reference

source_name: Cy5  labeled genomic DNA

tag: Cy5  labeled genomic DNA


title: GENOMIC DNA- E. histolytica (HM1:IMSS) 4ug with Petri lab DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39356.gif


title: GENOMIC DNA- E. dispar SAW760 4ug with  DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39360.gif


title: GENOMIC DNA- E. histolytica (HM1:IMSS)-experiment performed with 4ug

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38802.gif

source_name: Cy3 labelled pHOS reference

tag: Cy3 labelled pHOS reference

source_name: Cy5 labelled genomic DNA

tag: Cy5 labelled genomic DNA


title: A8, host/untreated (18 hpi), exp6

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25723.gif

source_name: untreated

tag: untreated

source_name: host

tag: host


title: 1223c overexpressed 10 hr

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43069.gif

source_name: RNA pool of all tp, three strains;2ug RNA

source_name: 1223c mt + 1223c OE 10hr;2ug RNA

tag: 1223c mt + 1223c OE 10hr;2ug RNA


title: 1223c mutant 2 hr

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43063.gif

tag: RNA pool of all tp, three strains;2ug RNA

source_name: 1223c mt + pRY108 2hr;2ug RNA

tag: 1223c mt + pRY108 2hr;2ug RNA


title: Strain 9802501, 10-3, MM091

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15287.gif

source_name: H37Rv genomic DNA control

tag: H37Rv genomic DNA control


title: mots, porB, rdxA, CEKG2C

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50583.gif

source_name: mots, porB, rdxA, S,CEKG2C

tag: mots, porB, rdxA, S,CEKG2C

source_name: mots, porB, rdxA, N,CEKG2C

tag: mots, porB, rdxA, N,CEKG2C


title: Strain CDC1551, 4-2, MM044

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15571.gif


title: Strain 9802501, 10-4, MM092

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15289.gif


title: mots, porB, rdxA, CEKG2A

description:
Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50582.gif

source_name: mots, porB, rdxA, S,CEKG2A

tag: mots, porB, rdxA, S,CEKG2A

source_name: mots, porB, rdxA, N,CEKG2A

tag: mots, porB, rdxA, N,CEKG2A


title: 1223c overexpressed 2 hr

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43067.gif

source_name: 1223c mt + 1223c OE 2hr;2ug RNA

tag: 1223c mt + 1223c OE 2hr;2ug RNA


title: Strain 9802501, 10-2, MM090

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15285.gif


title: Strain 9800608, 9-2, MM060

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15712.gif


title: Strain 9802501, 10-1, MM089

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15280.gif


title: A9, host/untreated (24 hpi), exp1

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20776.gif


title: 1223c overexpressed 6 hr

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43068.gif

source_name: 1223c mt + 1223c OE 6hr;2ug RNA

tag: 1223c mt + 1223c OE 6hr;2ug RNA


title: GENOMIC DNA-E. histolytica -Rahman hybed with 8ug genomic DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40778.gif

source_name: Cy5 labeled Rahman genomic DNA

tag: Cy5 labeled Rahman genomic DNA


title: B6, nonhost/untreated (18 hpi), exp2

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20795.gif

source_name: nonhost

tag: nonhost


title: A12, host/untreated (24 hpi), exp6

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25686.gif


title: A5, host/untreated (18 hpi), exp1

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20777.gif


title: Strain 9800608, 9-1, MM059

description:
Simple annotation: Strain comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15710.gif


title: BC6

status: Public on Aug 25 2005

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5276.gif

source_name: CRB1 reference

tag: CRB1 reference

source_name: BC6-HB high red background=HB

tag: BC6-HB high red background=HB


title: 1223c mutant 6 hr

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43064.gif

source_name: 1223c mt + pRY108 6hr;2ug RNA

tag: 1223c mt + pRY108 6hr;2ug RNA


title: BC18

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5303.gif

source_name: BC18-HB high red backround

tag: BC18-HB high red backround


title: BC121B-BE

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5815.gif

source_name: CR3 reference

tag: CR3 reference


title: BC706A-BE

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3302.gif


title: 1223c mutant 24 hr

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43066.gif

source_name: RNA pool of all tp, three strains;2ug RNA

source_name: 1223c mt +pRY108 24hr;2ug RNA

tag: 1223c mt +pRY108 24hr;2ug RNA


title: BC44

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5286.gif


title: BC11-FA

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3200.gif

source_name: BC11-FA has high red background

tag: BC11-FA has high red background


title: BC45

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5298.gif


title: BC702B-BE

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3206.gif


title: Normal Breast3

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3153.gif

source_name: NorBreast3-pool of 2 normal breasts

tag: NorBreast3-pool of 2 normal breasts


title: 1223c mutant 10 hr

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43065.gif

tag: RNA pool of all tp, three strains;2ug RNA

source_name: 1223c mt + pRY108 10hr;2ug RNA

tag: 1223c mt + pRY108 10hr;2ug RNA


title: BC4-LN4

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5804.gif


title: BC608B-BE

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3257.gif


title: BC20-FA

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/6656.gif

source_name: BC20-FA-HB high red background and weak red intensity


title: RV98 hpi 2

description:
Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32551.gif

source_name: Mock

tag: Mock

source_name: RV101 98 hpi

tag: RV101 98 hpi


title: GENOMIC DNA- E. histolytica (NIH200) 8ug genomic DNA

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40428.gif

source_name: Cy3 labeled pHOS reference DNA

tag: Cy3 labeled pHOS reference DNA

source_name: Cy5 labeled genomic NIH200 genomic DNA

tag: Cy5 labeled genomic NIH200 genomic DNA


title: fkh1,2 alpha factor 135 min

status: Public on Aug 24 2005

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/508.gif

source_name: fkh1,2 asynchronous

tag: fkh1,2 asynchronous

source_name: alpha factor release 135min

tag: alpha factor release 135min


title: RV98 hpi 1

description:
Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32546.gif


title: fkh1,2 alpha factor 150 min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/509.gif

source_name: alpha factor release 150 min

tag: alpha factor release 150 min


title: AD72 hpi 2

description:
Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32016.gif

source_name: AD169 72 hpi

tag: AD169 72 hpi


title: fkh1,2 alpha factor 075 min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/504.gif

source_name: alpha factor release 075 min

tag: alpha factor release 075 min


title: fkh1,2 alpha factor 060 min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/503.gif

source_name: alpha factor release 060 min

tag: alpha factor release 060 min


title: Y5 mRNP vs. Poly

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs//13490.gif

source_name: mRNP

tag: mRNP

source_name: Poly

tag: Poly


title: fkh1,2 alpha factor 165 min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/510.gif

source_name: alpha factor release 165 min

tag: alpha factor release 165 min


title: AD98 hpi 1

description:
Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32513.gif

source_name: AD169 98 hpi

tag: AD169 98 hpi


title: RV50 hpi 2

description:
Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31128.gif

source_name: RV101 50 hpi

tag: RV101 50 hpi


title: fkh1,2 alpha factor 090 min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/505.gif

source_name: alpha factor release 090 min

tag: alpha factor release 090 min


title: fkh1,2 alpha factor 030min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/502.gif

source_name: alpha factor release 030 min

tag: alpha factor release 030 min


title: AD72 hpi 1

description:
Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31791.gif

source_name: Mock

tag: Mock


title: AD98 hpi 2

description:
Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32567.gif


title: fkh1,2 alpha factor 120 min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/507.gif

source_name: alpha factor release 120 min

tag: alpha factor release 120 min


title: fkh1,2 alpha factor 105 min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/506.gif

source_name: alpha factor release 105 min

tag: alpha factor release 105 min


title: 1223c overexpressed 24 hr

description:
Simple annotation: Mutant vs Wild-type, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/43070.gif

source_name: RNA pool of all tp, three strains;2ug RNA

source_name: 1223c mt + 1223c OE 24hr;2ug RNA

tag: 1223c mt + 1223c OE 24hr;2ug RNA


title: fkh1,2 alpha factor 015 min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/501.gif

source_name: fkh1,2 asynchronous

tag: fkh1,2 asynchronous

source_name: alpha factor release 015 min

tag: alpha factor release 015 min


title: fkh1,2 alpha factor 000 min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/500.gif

source_name: alpha factor release 000 min

tag: alpha factor release 000 min


title: cell cycle-alpha factor, fkh1, fkh2 135min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2143.gif

source_name: Reference Pool

tag: Reference Pool

source_name: 135 min

tag: 135 min


title: fkh1,2 alpha factor 210 min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/121.gif

source_name: alpha factor release 210 min

tag: alpha factor release 210 min


title: AD50 hpi 2

description:
Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31247.gif

source_name: AD169 50 hpi

tag: AD169 50 hpi


title: fkh1,2 alpha factor 045 min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/565.gif

source_name: alpha factor release 045 min

tag: alpha factor release 045 min


title: cell cycle-alpha factor, fkh1, fkh2 000min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/487.gif

source_name: 000 min

tag: 000 min


title: cell cycle-alpha factor, fkh1, fkh2 015min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/486.gif

source_name: 015 min

tag: 015 min


title: RV72 hpi 1

description:
Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31845.gif

source_name: RV101 72 hpi

tag: RV101 72 hpi


title: RV72 hpi 2

description:
Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31947.gif


title: G0 mRNP vs. Poly

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs//13496.gif

source_name: mRNP

tag: mRNP

source_name: Poly

tag: Poly


title: RV50 hpi 1

description:
Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31125.gif

source_name: Mock

tag: Mock

source_name: RV101 50 hpi

tag: RV101 50 hpi


title: cell cycle-alpha factor, fkh1, fkh2 105min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/477.gif

source_name: 105 min

tag: 105 min


title: cell cycle-alpha factor, fkh1, fkh2 180min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/576.gif

source_name: 180 min

tag: 180 min


title: cell cycle-alpha factor, fkh1, fkh2 030min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/485.gif

source_name: 030 min

tag: 030 min


title: Yeast Membrane Bound Polysome Isolation #1

description:
Simple annotation: Polysomes, membrane-bound polysomes
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/308.gif

source_name: free polysomes

tag: free polysomes

source_name: membrane-bound polysomes

tag: membrane-bound polysomes


title: cell cycle-alpha factor, fkh1, fkh2 060min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/483.gif

source_name: Reference Pool

tag: Reference Pool

source_name: 060 min

tag: 060 min


title: macrophage 4b reloaded

description:
Simple annotation: Comparative genomics, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52141.gif

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: macrophage

tag: macrophage

source_name: media

tag: media


title: cell cycle-alpha factor, fkh1, fkh2 150min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/474.gif

source_name: 150 min

tag: 150 min


title: cell cycle-alpha factor, fkh1, fkh2 120min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/476.gif

source_name: 120 min

tag: 120 min


title: Y10 mRNP vs. Poly

description:
Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs//13493.gif


title: cell cycle-alpha factor, fkh1, fkh2 045min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/484.gif

source_name: 045 min

tag: 045 min


title: macrophage 2b reloaded

description:
Simple annotation: Comparative genomics, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52137.gif


title: cell cycle-alpha factor, fkh1, fkh2 075min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/482.gif

source_name: 075 min

tag: 075 min


title: BalbC_1a

description:
Simple annotation: Comparative genomics, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41501.gif

source_name: input

tag: input

source_name: output

tag: output


title: Balb pooled 2

description:
Simple annotation: Comparative genomics, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44730.gif


title: macrophage 5a reloaded

description:
Simple annotation: Comparative genomics, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52142.gif


title: macrophage 5b reloaded

description:
Simple annotation: Comparative genomics, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52143.gif


title: cell cycle-alpha factor, fkh1, fkh2 090min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/480.gif

source_name: 090 min

tag: 090 min


title: cell cycle-alpha factor, fkh1, fkh2 165min

description:
Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/473.gif

source_name: 165 min

tag: 165 min


title: Male 4 chip C

status: Public on Aug 23 2005

city: Denver

first: Melanie

last: Gubbels

state: CO

institute: University of Colorado Health Sciences Center

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

source_name: Whole spleen taken at 4 months of age


title: macrophage 6b reloaded

description:
Simple annotation: Comparative genomics, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52148.gif


title: macrophage 2a reloaded

description:
Simple annotation: Comparative genomics, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52136.gif


title: Male 3 chip C


title: BalbC_1b

description:
Simple annotation: Comparative genomics, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41629.gif


title: macrophage 6a reloaded

description:
Simple annotation: Comparative genomics, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52147.gif


title: Female 1 chip A

description:
Goal of experimet: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice.  (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference)

Whole spleen was taken from a pre-lupus (4 mo. old) (New Zealand Black x New Zealand White)F1 (BWF1) mouse.

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


title: Balb trash 2_pooled

description:
Simple annotation: Comparative genomics, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44724.gif


title: Male 1 chip C


title: Female 2 chip C

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

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


title: Male 2 chip C


title: Female 1 chip C

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

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


title: B5, nonhost/untreated (18 hpi), exp1

description:
Simple annotation: Pathogen, Disease response
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20772.gif

source_name: untreated

tag: untreated

source_name: nonhost

tag: nonhost