title: NRMRL test replicate02, EPA71 batch052704 430A chip


title: NRMRL test replicate01, EPA71 batch052704 430A chip

status: Public on Oct 21 2006

type: RNA

city: Cincinnati

first: Samuel

last: Hayes

state: OH

address: 26 W. Martin Luther King Dr.

country: USA

institute: United States Environmental Protection Agency

hyb_protocol: MAS 5.0 software EukGE-WS1

scan_protocol: MAS 5.0 with model 4500 scanner

data_processing: Microarray Suite (MAS) 5.0 software, target signal scaling 500; normalization 1; Alpha1 0.05; Alpha2 0.065; Tau 0.015; Gamma1L and 1H 0.0045; Gamma 2L and 2H 0.06; and Pertubation 1.1.

label: Streptavidin Phycoerythrin (SAPE)

molecule: total RNA

organism: Mus musculus

source_name: neonatal mouse small intestinal tissue, 5 hour infection

label_protocol: Affymetrix SOP, EukGE-WS2

extract_protocol: TriZol procedure

tag: Swiss Webster neonate, 5 days old


title: NRMRL cotrol replicate01, uninfected batch092303 430A chip

source_name: neonatal mouse small intestinal tissue, 5 hour


title: NRMRL test replicate02, EPA100 batch052704 430A chip

source_name: neonatal mouse small intetinal tissue, 5 hour infection


title: NRMRL test replicate02, EPA73 batch052704 430A chip


title: NRMRL test replicate04, EPA100 batch052704 430A chip

tag: Swiss Webster noenate, 5 days old


title: NRMRL test replicate03, EPA100 batch052704 430A chip


title: NRMRL test replicate01, EPA73 batch052704 430A chip


title: NRMRL test replicate03, EPA71 batch052704 430A chip


title: NRMRL test replicate03, EPA1HK batch052704 430A chip

data_processing: MAS 5.0 software, target signal scaling 500; normalization 1; Alpha1 0.05; Alpha2 0.065; Tau 0.015; Gamma1L and 1H 0.0045; Gamma 2L and 2H 0.06; and Pertubation 1.1.

source_name: neonatal mouse small intestinal tissue, 5 hour treatment


title: NRMRL test replicate05, EPA72 batch052704 430A chip


title: NRMRL test replicate04, EPA1HK batch052704 430A chip


title: NRMRL test replicate05, EPA100 batch052704 430A chip


title: NRMRL replicate03, EPA72 batch052704 430A chip

source_name: Neonatal mouse small intestinal tissue, 5 hour infection


title: NRMRL test replicate01, EPA100 batch052704 430A chip


title: NRMRL test replicate02, EPA72 batch052704 430A chip

source_name: neontal mouse small intestinal tissue, 5 hour infection


title: NRMRL test replicate04, EPA72 batch052704 430A chip


title: NRMRL test replicate05, EPA1HK batch052704 430A chip


title: NRMRL test replicate01, EPA72 batch052704 430A chip


title: NRMRL test replicate02, EPA73 batch072104 430A chip

source_name: mouse small intestinal cell culture, 5 hour infection

tag: MICcl2 cell line


title: NRMRL control replicate05, uninfected batch052704 430A chip

source_name: neonatal mouse small intestinal tissue, 5 hours


title: NRMRL control replicate04, uninfected batch052704 430A chip


title: NRMRL test replicate01, EPA1HK batch052704 430A chip


title: NRMRL test replicate02, EPA1HK batch052704 430A chip


title: NRMRL control replicate02, uninfected batch052704 430A chip


title: NRMRL control replicate02, uninfected batch092304 430A chip


title: NRMRL control replicate04, uninfected batch092304 430A chip


title: NRMRL control replicate03, uninfected batch092304 430A chip


title: NRMRL control replicate01, uninfected batch052704 430A chip


title: NRMRL control replicate01, uninfected batch092304 430A chip


title: NRMRL test replicate05, EPA63 batch092304 430A chip


title: NRMRL test replicate02, EPA63 batch092304 430A chip

tag: Swiss Webster neonates, 5 days old


title: NRMRL test replicate04, EPA61 batch092304 430A chip


title: NRMRL test replicate05, EPA61 batch092304 430A chip


title: NRMRL test replicate04, EPA63 batch092304 430A chip


title: NRMRL test replicate03, EPA61 batch092304 430A chip


title: NRMRL control replicate03, uninfected batch052704 430A chip


title: NRMRL test replicate01, EPA61 batch093404 430A chip


title: NRMRL test replicate01, EPA63 batch092304 430A chip


title: NRMRL test replicate03, EPA63 batch092304 430A chip


title: Microarray I vs J from Loss of the RNA-binding protein Kep1

city: Sherbrooke

first: Marco

last: Di Fruscio

state: Quebec

address: 2500 boul. Université

department: Biologie

country: Canada

institute: Université de Sherbrooke

description: Canadian Drosophila Microarray Center

data_processing: Canadian Drosophila Microarray Center

organism: Drosophila melanogaster

source_name: wild-type w1118 male RNA

label_protocol: Labelling carried out at the Canadian Drosophila Microarray Center, Neal et al 2003 Genome 46, 879-892

extract_protocol: Trizol followed by QIAGEN column

tag: 3-4 day old heads

source_name: kep1-/kep1- male RNA


title: Microarray 1 from Loss of the RNA-binding protein Kep1

description: Canadian Drosophila Microarray Center

hyb_protocol: Canadian Drosophila Microarray Center, Neal et al 2003 Genome 46, 879-892

source_name: wild-type w1118  male RNA

tag: RNA isolated from 3-4 day old males


title: 2005-11-08 GB2 2

status: Public on Oct 20 2006

city: Stanford

first: Anna

last: Brotcke

state: CA

department: Microbiology and Immunology

institute: Stanford University

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65307.gif; format: GIF

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

organism: Francisella tularensis

source_name: Ref

tag: Ref

source_name: Timepoints

tag: Timepoints


title: NRMRL test replicate02, EPA61 batch092304 430A chip


title: 2005-11-08 GB2 1

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65306.gif; format: GIF


title: 2005-11-08 U112 6

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65304.gif; format: GIF


title: Microarry 3 from Loss of the RNA-binding protein Kep1

description: Canadian Drosophila Microarray Center

scan_protocol: Canadian Drosophila Microarray Center, Neal et al 2003 Genome 46, 879-892


title: 2005-11-08 U112 5

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65302.gif; format: GIF


title: 2005-11-08 GB2 3

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65309.gif; format: GIF


title: 2005-1-8-mglA(10b)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65123.gif; format: GIF


title: 2005-1-8-mglA(9b)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65122.gif; format: GIF


title: 2005-11-08 U112 7

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65305.gif; format: GIF


title: 2005-1-8-mglA(7a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58827.gif; format: GIF


title: 2005-1-8-U112(8a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58826.gif; format: GIF


title: 2005-11-08 U112 4

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65301.gif; format: GIF


title: 2005-11-08 U112 3

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65300.gif; format: GIF


title: 2005-1-8-U112(9a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58828.gif; format: GIF


title: 2005-1-8-mglA(8b)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65121.gif; format: GIF


title: 2005-1-8-U112(6a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58822.gif; format: GIF


title: 2005-1-8-mglA(4a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58821.gif; format: GIF


title: 2005-1-8-mglA(3a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59224.gif; format: GIF


title: 2005-1-8-mglA(6a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58825.gif; format: GIF


title: 2005-1-8-mglA(1a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59223.gif; format: GIF


title: 2005-1-8-U112(7a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58824.gif; format: GIF


title: 2005-1-8-U112(10b)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65120.gif; format: GIF


title: 2005-1-8-U112(5a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58819.gif; format: GIF


title: 2005-11-08 GB2 6

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65312.gif; format: GIF


title: 2005-11-08 GB2 5

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65311.gif; format: GIF


title: 2005-11-08 GB2 4

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65310.gif; format: GIF


title: 2005-1-8-mglA(2a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58818.gif; format: GIF


title: 2005-11-08 GB2 7

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65314.gif; format: GIF


title: 2005-1-8-mglA(5b)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59225.gif; format: GIF


title: 2005-1-8-U112(4a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58817.gif; format: GIF


title: 2005-11-08 U112 2

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65299.gif; format: GIF


title: 2005-1-8-U112(1a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58813.gif; format: GIF


title: The Identification of gene expression changes in human embryonic fibroblast cells, background. Sample B

city: Copenhagen

first: Adrian

middle: P.

last: Bracken

address: Fruebjergvej 3

country: Denmark

institute: Biotech Research & Innovation Centre (BRIC)

description: TIG3  diploid lung embryonic fibroblasts were untreated (MOCK). After 44 hours expression analysis was performed.

hyb_protocol: Hybridization procedures and parameters: Hybridization mix for target dilution (100 mM MES, 1 M [Na +], 20 mM EDTA, 0.01% Tween 20) was prepared as indicated by Affymetrix, including pre-mixed biotin-labeled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat# 900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM respectively. Targets were diluted in hybridization buffer at a concentration of 150µg/ml and denatured at 99°C prior to introduction into the GeneChip cartridge. Three copies of the complete GeneChip HG-U133 set (HG-U133A, HG-U133B) were then hybridized with each biotin-labeled target. Hybridizations were performed for 14-16 hours at 45°C in a rotisserie oven. GeneChip cartridges were washed and stained in the Affymetrix fluidics station following the EukGE-WS2 standard protocol (including Antibody Amplification): 1.	Wash 10 cycles of 2 mixes/cycle with Wash Buffer A (6X SSPE, 0.01% Tween 20) at 25°C 2.	Wash 4 cycles of 15 mixes/cycle with Wash Buffer B (100 mM MES, 0.1 M [Na+], 0.01% Tween 20) at 50°C 3.	Stain the probe array for 10 minutes in SAPE solution (10 µg/mL SAPE in 100 mM MES, 1 M [Na +], 0.05% Tween 20, 2 mg/mL BSA) at 25°C 4.	Wash 10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C 5.	Stain the probe array for 10 minutes in antibody solution (Normal Goat IgG 0.1 mg/mL, 6.	Biotinylated antibody 3 µg/mL, 100 mM MES, 1 M [Na +], 0.05% Tween 20, 2 mg/mL BSA) at 25°C 7.	Stain the probe array for 10 minutes in SAPE solution at 25°C 8.	Final Wash 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C

scan_protocol: Images were scanned using an Affymetrix GeneArray Scanner, using default parameters. The resulting images were analysed using Microarray Suite version 5 (MASv5), Affymetrix cat# 690018.

data_processing: Raw signal

label: Biotin

organism: Homo sapiens

source_name: TIG3 embryonic diploid fibroblasts

label_protocol: Biotin-labelled cRNA targets were synthesized starting from 5µg of total RNA. Double stranded cDNA synthesis was performed with GIBCO SuperScript Custom cDNA Synthesis Kit, and biotin-labelled antisense RNA was transcribed in vitro using Ambion’s In Vitro Transcription System, including Bio-11-UTP and Bio-11-CTP (NEN Life Sciences, PerkinElmer Inc, Boston, Massachusetts, USA) in the reaction. All steps of the labelling protocol were performed as suggested by Affymetrix (GeneChip® Expression Analysis Technical Manual ). The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2µg aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150µg/ml.

growth_protocol: TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. Cells were transfected with mock(background) and harvested for preparation of RNA after 44 hours.

extract_protocol: Total RNA was extracted using the RNeasy mini/midi Kit (RNeasy Mini/Midi Kit, Qiagen). For each siRNA transfection, an RNA pool was obtained by mixing equal quantities of total RNA from each of the six independent RNA extractions.

tag: TIG3 diploid lung embryonic fibroblasts, background.


title: 2005-11-08 U112 1

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65298.gif; format: GIF


title: The Identification of gene expression changes in human embryonic fibroblast cells depleted of SUZ12. Sample A

description: TIG3 diploid lung embryonic fibroblasts were transfected with siRNA oligos specific for the Polycomb protein SUZ12. After 44 hours expression analysis was performed.

hyb_protocol: Hybridization procedures and parameters: Hybridization mix for target dilution (100 mM MES, 1 M [Na +], 20 mM EDTA, 0.01% Tween 20) was prepared as indicated by Affymetrix, including pre-mixed biotin-labeled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat# 900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM respectively. Targets were diluted in hybridization buffer at a concentration of 150µg/ml and denatured at 99°C prior to introduction into the GeneChip cartridge. Three copies of the complete GeneChip HG-U133 set (HG-U133A, HG-U133B) were then hybridized with each biotin-labeled target. Hybridizations were performed for 14-16 hours at 45°C in a rotisserie oven. GeneChip cartridges were washed and stained in the Affymetrix fluidics station following the EukGE-WS2 standard protocol (including Antibody Amplification): 1. Wash 10 cycles of 2 mixes/cycle with Wash Buffer A (6X SSPE, 0.01% Tween 20) at 25°C 2. Wash 4 cycles of 15 mixes/cycle with Wash Buffer B (100 mM MES, 0.1 M [Na+], 0.01% Tween 20) at 50°C 3. Stain the probe array for 10 minutes in SAPE solution (10 µg/mL SAPE in 100 mM MES, 1 M [Na +], 0.05% Tween 20, 2 mg/mL BSA) at 25°C 4. Wash 10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C 5. Stain the probe array for 10 minutes in antibody solution (Normal Goat IgG 0.1 mg/mL, 6. Biotinylated antibody 3 µg/mL, 100 mM MES, 1 M [Na +], 0.05% Tween 20, 2 mg/mL BSA) at 25°C 7. Stain the probe array for 10 minutes in SAPE solution at 25°C 8. Final Wash 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C

scan_protocol: Genechip array scan Images were scanned using an Affymetrix GeneArray Scanner, using default parameters. The resulting images were analysed using Microarray Suite version 5 (MASv5), Affymetrix cat# 690018.

source_name: TIG3 diploid lung embryonic fibroblasts

growth_protocol: TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were transfected with siRNA oligonucleotides specific for SUZ12 and harvested for preparation of RNA after 44 hours.

tag: TIG3 diploid lung embryonic fibroblasts


title: The Identification of gene expression changes in human embryonic fibroblast cells depleted of EED. Sample C

description: TIG3 diploid lung embryonic fibroblasts were transfected with siRNA oligos specific for the Polycomb protein EED. After 44 hours expression analysis was performed.

growth_protocol: TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were transfected with siRNA oligonucleotides specific for EED and harvested for preparation of RNA after 44 hours.


title: The Identification of gene expression changes in human embryonic fibroblast cells, background. Sample A

description: TIG3  diploid lung embryonic fibroblasts were transfected with siRNA oligos specific for MOCK. After 44 hours expression analysis was performed.

source_name: TIG3  diploid lung embryonic fibroblasts

treatment_protocol: Cells were transfected with mock(background) and harvested for preparation of RNA after 44 hours.


title: The Identification of gene expression changes in human embryonic fibroblast cells, background. Sample C

description: TIG3  diploid lung embryonic fibroblasts were non-transfected. After 44 hours expression analysis was performed.


title: The Identification of gene expression changes in human embryonic fibroblast cells depleted of EZH2. Sample C

description: TIG3 diploid lung embryonic fibroblasts were transfected with siRNA oligos specific for the Polycomb protein EZH2. After 44 hours expression analysis was performed.

growth_protocol: TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were transfected with siRNA oligonucleotides specific for EZH2 and harvested for preparation of RNA after 44 hours.


title: The Identification of gene expression changes in human embryonic fibroblast cells depleted of EED. Sample B

treatment_protocol: TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were transfected with siRNA oligonucleotides specific for EED and harvested for preparation of RNA after 44 hours.


title: The Identification of gene expression changes in human embryonic fibroblast cells depleted of SUZ12. Sample B

treatment_protocol: TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were transfected with siRNA oligonucleotides specific for SUZ12 and harvested for preparation of RNA after 44 hours.


title: mouse, E14.5 wild type whole embryo, microarray data set 1

city: Göttingen

first: Murat

last: Cankaya

address: Am Faßberg 11

department: Department of Genes and Behavior

country: Germany

institute: Max Planck Institute for Biophysical Chemistry

description: mouse, E14.5 wild type whole embryo

data_processing: Primary data analysis with GCOS 1.3

label: biotin

source_name: E14.5 mouse embryo

extract_protocol: Total RNA was isolated from mouse embryo with RNAzol


title: 2005-1-8-U112(2a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58815.gif; format: GIF


title: 2005-1-8-U112(3a)

description:
Simple annotation: Pathogen, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58816.gif; format: GIF


title: mouse, E14.5 wild type whole embryo, microarray data set 2

description: mouse, E14.5 wild type whole embryo


title: The Identification of gene expression changes in human embryonic fibroblast cells depleted of BMI-1. Sample A

description: TIG3  diploid lung embryonic fibroblasts were transfected with siRNA oligos specific for the Polycomb protein BMI-1. After 44 hours expression analysis was performed.

treatment_protocol: TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were transfected with siRNA oligonucleotides specific for BMI-1 and harvested for preparation of RNA after 44 hours.


title: The Identification of gene expression changes in human embryonic fibroblast cells depleted of SUZ12. Sample C


title: The Identification of gene expression changes in human embryonic fibroblast cells depleted of BMI-1. Sample C

description: TIG3 diploid lung embryonic fibroblasts were transfected with siRNA oligos specific for the Polycomb protein BMI-1. After 44 hours expression analysis was performed.

growth_protocol: TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were transfected with siRNA oligonucleotides specific for BMI-1 and harvested for preparation of RNA after 44 hours.


title: The Identification of gene expression changes in human embryonic fibroblast cells depleted of EZH2. Sample B

treatment_protocol: TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were transfected with siRNA oligonucleotides specific for EZH2 and harvested for preparation of RNA after 44 hours.


title: The Identification of gene expression changes in human embryonic fibroblast cells depleted of EZH2. Sample A


title: The Identification of gene expression changes in human embryonic fibroblast cells depleted of EED. Sample A


title: The Identification of gene expression changes in human embryonic fibroblast cells depleted of BMI-1. Sample B


title: Transcriptional profile of Candida glabrata ingested by macrophage cells for 6 hours (Experiment 3-2)

status: Public on Oct 19 2006

city: Baltimore

first: Brendan

last: Cormack

state: MD

address: Hunterian Building 617, 725 N. Wolfe St.

department: Molecular Biology & Genetics

institute: Johns Hopkins Univ. School of Medicine

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM140634.

hyb_protocol: Both Cy5- and Cy3- cDNA probes were resuspened into hybridization buffer (35% formamide, 5*SSC, 0.1%SDS, 0.1 mg/ml denatured salmon sperm DNA) and combined to a total volume of 40 ul. The probe mix was denatured at 100 C for 10 s and quickly cooled on ice, then it was added on a microarray slides. The slides was covered with a cover glass and incubated in a chamber (Corning) at 42 C for 16-18 hrs. The washing protocol follows the manual for UltraGAPS coated slides (Corning).

scan_protocol: Hybridized slides was scaned by Axon 4000B microarray scanner with 100% power and PMT ranging 600-800. Data were acquired by Axon GenePix 5.0 software.

data_processing: The median signal intensity captured from Cy5-channel (F635) and from Cy3-channel (F532) was used to calculate the C. glabrata gene expression ratio (Macrophage ingested/medium control

organism: Nakaseomyces glabratus

source_name: C. glabrata medium control

label_protocol: 20 ug of total RNA was used to synthesize Cy5-cDNA probes with an anchor primer [(dT)18(dA/dG/dC)] in the presence of Cy5-dCTP (PerkinElmer) using SuperscriptTM III reverse transcriptase (Invitrogen). The probe was purified using MinElute TM reaction Cleanup kit (Qiagen) and vaccum dried.

extract_protocol: C. glabrata cells were disrupted with 0.5-mm glass beads (Fisher Scientific) in the presence of guanidium-isothiocyanate (GITC), and the total RNA was isolated by acid phenol extraction. The RNA was further purified by RNeasy Mini kit (Qiagen).

treatment_protocol: C. glarata cells cultured in DMEM supplemented with 10 % FBS for 6 hrs.

tag: A wild type strain of C. glabrata, Cg462 was used in this experiment and it is routinely cultured in YPD medium at 30 C.

source_name: C. glabrata ingested by murine macrophage-like cells J774A.1 for 6 hours

label_protocol: see in channel 1

extract_protocol: see in channel 1

treatment_protocol: J774A.1 macrophage-like cells were seeded in a 175 cm2 tissue culture flasks and cultured for 16-18 hrs till confluency. Log phase C. glabrata cells (about 2*107 cells/flask) were added onto the macrophage cells to a MOI of 1:1. The flask was spun down for 1 min at 1,000 rpm to bring the yeast cells down. The flask was incubated at 37 C. After 1 hr, the yeast cells that remained outside of macrophages were washed off with warm PBS, and fresh medium was added. At hour 6, the macrophages were lysed in ice-cold water containing RNase cocktail (Ambion Biotech)(to degrade the released macrophage RNA) for 5 min. The lysate was quickly spun down, washed twice with RNase-free water containing protectRNA TM RNase inhibitor (Sigma). Finally the yeast cell pellets from 6 flasks (1*108 cells total) was quickly frozen in liquid nitrogen for RNA prep.

tag: Murine macrophage-like cell line J774A.1 was purchased from ATCC and it is routinely cultured at 37 C in humidified 5 % CO2 atmosphere in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS).


title: Transcriptional profile of Candida glabrata ingested by macrophage cells for 6 hours (Experiment 1-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM140627.


title: Transcriptional profile of Candida glabrata ingested by macrophage cells for 6 hours (Experiment 3-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM140635.

growth_protocol: J774A.1 macrophage-like cells were seeded in a 175 cm2 tissue culture flasks and cultured for 16-18 hrs till confluency. Log phase C. glabrata cells (about 2*10 7 cells/flask) were added onto the macrophage cells to a MOI of 1:1. The flask was spun down for 1 min at 1,000 rpm to bring the yeast cells down. The flask was incubated at 37 C. After 1 hr, the yeast cells that remained outside of macrophages were washed off with warm PBS, and fresh medium was added. At hour 6, the macrophages were lysed in ice-cold water containing RNase cocktail (Ambion Biotech)(to degrade the released macrophage RNA) for 5 min. The lysate was quickly spun down, washed twice with RNase-free water containing protectRNA TM RNase inhibitor (Sigma). Finally the yeast cell pellets from 6 flasks (1*10 8 cells total) was quickly frozen in liquid nitrogen for RNA prep.

tag: see in channel 1


title: Transcriptional profile of Candida glabrata ingested by macrophage cells for 2 hours (Experiment 3-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM140625.

treatment_protocol: C. glarata cells cultured in DMEM supplemented with 10 % FBS for 2 hrs.

source_name: C. glabrata ingested by murine macrophage-like cells J774A.1 for 2 hours

treatment_protocol: J774A.1 macrophage-like cells were seeded in a 175 cm2 tissue culture flasks and cultured for 16-18 hrs till confluency. Log phase C. glabrata cells (about 2*107 cells/flask) were added onto the macrophage cells to a MOI of 1:1. The flask was spun down for 1 min at 1,000 rpm to bring the yeast cells down. The flask was incubated at 37 C. After 1 hr, the yeast cells that remained outside of macrophages were washed off with warm PBS, and fresh medium was added. At hour 2, the macrophages were lysed in ice-cold water containing RNase cocktail (Ambion Biotech)(to degrade the released macrophage RNA) for 5 min. The lysate was quickly spun down, washed twice with RNase-free water containing protectRNA TM RNase inhibitor (Sigma). Finally the yeast cell pellets from 6 flasks (1*108 cells total) was quickly frozen in liquid nitrogen for RNA prep.


title: Transcriptional profile of Candida glabrata ingested by macrophage cells for 6 hours (Experiment 1-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM140631.

treatment_protocol: J774A.1 macrophage-like cells were seeded in a 175 cm2 tissue culture flasks and cultured for 16-18 hrs till confluency. Log phase C. glabrata cells (about 2*10 7 cells/flask) were added onto the macrophage cells to a MOI of 1:1. The flask was spun down for 1 min at 1,000 rpm to bring the yeast cells down. The flask was incubated at 37 C. After 1 hr, the yeast cells that remained outside of macrophages were washed off with warm PBS, and fresh medium was added. At hour 6, the macrophages were lysed in ice-cold water containing RNase cocktail (Ambion Biotech)(to degrade the released macrophage RNA) for 5 min. The lysate was quickly spun down, washed twice with RNase-free water containing protectRNA TM RNase inhibitor (Sigma). Finally the yeast cell pellets from 6 flasks (1*10 8 cells total) was quickly frozen in liquid nitrogen for RNA prep.


title: Transcriptional profile of Candida glabrata ingested by macrophage cells for 6 hours (Experiment 2-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM140633.


title: Transcriptional profile of Candida glabrata ingested by macrophage cells for 6 hours (Experiment 2-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM140632.


title: Transcriptional profile of Candida glabrata ingested by macrophage cells for 2 hours (Experiment 2-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM140621.

data_processing: The median signal intensity captured from Cy5-channel (F635) and from Cy3-channel (F532) was used to calculate the C. glabrata gene expression ratio (Macrophage ingested/medium control).

treatment_protocol: same as in GSM140373


title: Transcriptional profile of Candida glabrata ingested by macrophage cells for 2 hours (Experiment 2-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM140375.


title: Transcriptional profile of Candida glabrata ingested by macrophage cells for 2 hours (Experiment 3-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM140626.


title: Transcriptional profile of Candida glabrata ingested by macrophage cells for 2 hours (Experiment 1-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM140373.


title: Transcriptional profile of Candida glabrata ingested by macrophage cells for 2 hours (Experiment 1-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM140374.

data_processing: The median signal intensity captured from Cy5-channel (F635) and from Cy3-channel (F532) was used to calculate the C. glabrata gene expression ratio (Macrophage ingested/medium control)


title: Expression data of CCMS_52

status: Public on Oct 18 2006

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

country: Japan

institute: University of Tokyo

description: MSS, proximal

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturer's instructions.

tag: Tissue

value: Colorecal Cancer


title: Expression data of CCMS_55

description: MSS, proximal


title: Expression data of CCMS_53

description: MSS, proximal


title: Expression data of CCMS_54

description: MSI, proximal


title: Beta_ChIP_control_B_cy3

type: genomic

city: Boston

first: Nikos

last: Reppas

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard University

description: DNA input for ChIP

hyb_protocol: Labeled DNA was hybridized and scanned using proprietary methods (NimbleGen).

data_processing: Linearly scaled so that intensity values in Sigma70_ChIP_control_A_cy3, Sigma70_ChIP_A_cy5, Sigma70_ChIP_control_B_cy3, Sigma70_ChIP_B_cy5, Beta_ChIP_control_A_cy3, Beta_ChIP_A_cy5, Beta_ChIP_control_B_cy3, Beta_ChIP_B_cy5 are comparable

molecule: genomic DNA

organism: Escherichia coli

source_name: E. coli MG1655

label_protocol: ChIP DNA was first denatured and 2-cycle-amplified amplified using primer A (5'-GTTTCCCAGTCACGATCNNNNNNNNN); the resulting DNA was then subjected to a 35-round amplification using primer B (5'-TCCCAGTCACGATC).

extract_protocol: Cells were fixed in 1% formaldehyde at room temperature for 20 min, quenched with glycine, and lysed. Chromatin was pelleted and solublized by sonication.

tag: Strain MG1655


title: Sigma70_ChIP_A_cy5

description: ChIP DNA

scan_protocol: Labeled DNA was hybridized and scanned using proprietary methods (NimbleGen).

extract_protocol: Cells were fixed in 1% formaldehyde at room temperature for 20 min, quenched with glycine, and lysed. Chromatin was pelleted and solublized by sonication. Crosslinked chromatin was then immunoprecipitated.


title: Beta_ChIP_A_cy5

description: ChIP DNA


title: Beta_ChIP_control_A_cy3

description: DNA input for ChIP


title: Sigma70_ChIP_B_cy5

description: ChIP DNA


title: Sigma70_ChIP_control_A_cy3

description: DNA input for ChIP


title: cDNA_B_cy5

description: Body-labeled cDNA

data_processing: Linearly scaled so that intensity values in gDNA_A_cy5, cDNA_A_cy3, gDNA_B_cy3, and cDNA_B_cy5 are comparable

source_name: E. coli MG1655 RNA

label_protocol: cDNA was labeled with functionalized fluorophore.

extract_protocol: Total RNA was purified on a RNeasy columns (Qiagen); ribosomal RNAs were removed with the MicroExpress kit (Ambion). The resulting RNA was reverse transcribed with SuperScript II reverse transcriptase (Invitrogen) + random hexamers + dNTP mix containing aminoallyl-dUTP.


title: Sigma70_ChIP_control_B_cy3

description: DNA input for ChIP


title: cDNA_A_cy3

description: Body-labeled cDNA


title: Expression data of CCMS_51

description: MSS, proximal


title: Expression data of CCMS_46

description: MSS, distal


title: gDNA_B_cy3

description: Body-labeled hybridization efficiency control for cDNA

source_name: E. coli MG1655 genomic DNA

label_protocol: Sheared genomic DNA was amplified using Klenow DNA polymerase + random hexamers + dNTP mix containing aminoallyl-dUTP; amplified DNA was then labeled with functionalized fluorophore.

extract_protocol: Genomic DNA was purified using a 20/G genomic-tip kit (Qiagen) according to manufacturer's instructions and was sonicated to an average size of ~500 bp.


title: Expression data of CCMS_45

description: MSS, distal


title: gDNA_A_cy5


title: Beta_ChIP_B_cy5

description: ChIP DNA


title: 677 Barrett's(S)

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54526.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.74; Parameter Scan Time = 09:55:18; Parameter PMT Volts = 580; Parameter Scan Date = 2004-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 177469; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.74; Parameter Scan Time = 09:55:18; Parameter PMT Volts = 730; Parameter Scan Date = 2004-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 542273; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.95; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao

source_name: ref

label_protocol: not provided

extract_protocol: not provided

tag: ref


title: 677Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54525.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 6040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.34; Parameter Scan Time = 10:27:01; Parameter PMT Volts = 580; Parameter Scan Date = 2004-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 177039; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.34; Parameter Scan Time = 10:27:01; Parameter PMT Volts = 740; Parameter Scan Date = 2004-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 541843; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.99; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 667 Normal

description:
Simple annotation: Drug resistance, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54518.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.22; Parameter Scan Time = 10:14:57; Parameter PMT Volts = 580; Parameter Scan Date = 2004-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 177027; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.22; Parameter Scan Time = 10:14:57; Parameter PMT Volts = 670; Parameter Scan Date = 2004-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 541831; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 677Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54527.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.55; Parameter Scan Time = 09:42:10; Parameter PMT Volts = 610; Parameter Scan Date = 2004-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 177456; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.55; Parameter Scan Time = 09:42:10; Parameter PMT Volts = 710; Parameter Scan Date = 2004-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 542260; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.91; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 679 Barrett's(L)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54509.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.53; Parameter Scan Time = 12:15:27; Parameter PMT Volts = 620; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 173933; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.53; Parameter Scan Time = 12:15:27; Parameter PMT Volts = 750; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 538736; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.04; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 667 Barrett's(S)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54519.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 5640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.58; Parameter Scan Time = 11:12:26; Parameter PMT Volts = 580; Parameter Scan Date = 2004-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 177084; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.58; Parameter Scan Time = 11:12:26; Parameter PMT Volts = 770; Parameter Scan Date = 2004-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 541888; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.00; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 677Barrett's(S)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54524.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 6280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.68; Parameter Scan Time = 11:28:15; Parameter PMT Volts = 580; Parameter Scan Date = 2004-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 177101; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.68; Parameter Scan Time = 11:28:15; Parameter PMT Volts = 870; Parameter Scan Date = 2004-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 541904; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.99; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: N-4 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61459.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.65; Parameter Scan Time = 11:57:43; Parameter PMT Volts = 620; Parameter Scan Date = 2005-05-21; Parameter Pixel Size = 10; Parameter Laser on time = 217795; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.65; Parameter Scan Time = 11:57:43; Parameter PMT Volts = 660; Parameter Scan Date = 2005-05-21; Parameter Pixel Size = 10; Parameter Laser on time = 582599; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.07; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 681Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54504.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6840; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.91; Parameter Scan Time = 10:57:06; Parameter PMT Volts = 600; Parameter Scan Date = 2004-07-27; Parameter Pixel Size = 10; Parameter Laser on time = 178193; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.91; Parameter Scan Time = 10:57:06; Parameter PMT Volts = 670; Parameter Scan Date = 2004-07-27; Parameter Pixel Size = 10; Parameter Laser on time = 542997; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: T-6 AdenoCa

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61465.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.10; Parameter Scan Time = 12:39:25; Parameter PMT Volts = 640; Parameter Scan Date = 2005-05-21; Parameter Pixel Size = 10; Parameter Laser on time = 217837; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.10; Parameter Scan Time = 12:39:25; Parameter PMT Volts = 710; Parameter Scan Date = 2005-05-21; Parameter Pixel Size = 10; Parameter Laser on time = 582640; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.08; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 667 Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54522.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 6040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.50; Parameter Scan Time = 10:58:33; Parameter PMT Volts = 580; Parameter Scan Date = 2004-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 177069; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.50; Parameter Scan Time = 10:58:33; Parameter PMT Volts = 800; Parameter Scan Date = 2004-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 541873; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 677 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54523.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 6040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.44; Parameter Scan Time = 10:40:03; Parameter PMT Volts = 580; Parameter Scan Date = 2004-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 177051; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.44; Parameter Scan Time = 10:40:03; Parameter PMT Volts = 800; Parameter Scan Date = 2004-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 541855; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: B-6 Barrett's

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61464.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 4840; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 16:45:32; Parameter PMT Volts = 530; Parameter Scan Date = 2005-05-24; Parameter Pixel Size = 10; Parameter Laser on time = 40431; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 16:45:32; Parameter PMT Volts = 770; Parameter Scan Date = 2005-05-24; Parameter Pixel Size = 10; Parameter Laser on time = 212630; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 676 Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54507.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 34.15; Parameter Scan Time = 12:28:01; Parameter PMT Volts = 580; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 179651; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 34.15; Parameter Scan Time = 12:28:01; Parameter PMT Volts = 680; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 544455; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.58; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: B-1 Barrett's

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61453.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.13; Parameter Scan Time = 11:18:10; Parameter PMT Volts = 610; Parameter Scan Date = 2005-05-19; Parameter Pixel Size = 10; Parameter Laser on time = 217446; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.13; Parameter Scan Time = 11:18:10; Parameter PMT Volts = 630; Parameter Scan Date = 2005-05-19; Parameter Pixel Size = 10; Parameter Laser on time = 582250; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.89; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 679 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54508.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 6720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.44; Parameter Scan Time = 11:58:28; Parameter PMT Volts = 630; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 173916; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.44; Parameter Scan Time = 11:58:28; Parameter PMT Volts = 940; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 538720; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 671Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54490.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.66; Parameter Scan Time = 13:51:48; Parameter PMT Volts = 600; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 178874; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.15; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.66; Parameter Scan Time = 13:51:48; Parameter PMT Volts = 630; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 543678; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: T-1 AdenoCa

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61454.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.91; Parameter Scan Time = 11:05:17; Parameter PMT Volts = 610; Parameter Scan Date = 2005-05-19; Parameter Pixel Size = 10; Parameter Laser on time = 217433; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.91; Parameter Scan Time = 11:05:17; Parameter PMT Volts = 620; Parameter Scan Date = 2005-05-19; Parameter Pixel Size = 10; Parameter Laser on time = 582237; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.89; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 678 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54513.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 6720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.16; Parameter Scan Time = 11:04:34; Parameter PMT Volts = 640; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 173862; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.16; Parameter Scan Time = 11:04:34; Parameter PMT Volts = 660; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 538666; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.04; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 677 Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54502.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 7000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.26; Parameter Scan Time = 14:50:44; Parameter PMT Volts = 590; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 179794; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.26; Parameter Scan Time = 14:50:44; Parameter PMT Volts = 660; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 544598; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.73; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 678 Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54515.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 6720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.35; Parameter Scan Time = 11:42:05; Parameter PMT Volts = 640; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 173899; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.21; Parameter Scan Time = 11:22:22; Parameter PMT Volts = 660; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 538684; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: T-4 AdenoCa

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61460.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.39; Parameter Scan Time = 11:39:16; Parameter PMT Volts = 640; Parameter Scan Date = 2005-05-21; Parameter Pixel Size = 10; Parameter Laser on time = 217777; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.39; Parameter Scan Time = 11:39:16; Parameter PMT Volts = 630; Parameter Scan Date = 2005-05-21; Parameter Pixel Size = 10; Parameter Laser on time = 582581; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.99; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: NGM versus CeMM growth #3

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33640.gif

scan_protocol: not provided

organism: Caenorhabditis elegans

source_name: NGM grown mixed stage animals

tag: Plate Grown

source_name: CeMM grown mixed stage animals

tag: Culture Grown


title: 676 Barrett's(L)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54506.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1600, 5360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.61; Parameter Scan Time = 12:14:57; Parameter PMT Volts = 560; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 179639; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.57; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.61; Parameter Scan Time = 12:14:57; Parameter PMT Volts = 780; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 544443; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.63; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 683 Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54485.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 6400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.36; Parameter Scan Time = 12:47:13; Parameter PMT Volts = 580; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 178809; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.36; Parameter Scan Time = 12:47:13; Parameter PMT Volts = 630; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 543613; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: N-5 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61461.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 5040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.18; Parameter Scan Time = 15:13:32; Parameter PMT Volts = 530; Parameter Scan Date = 2005-05-24; Parameter Pixel Size = 10; Parameter Laser on time = 40348; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.18; Parameter Scan Time = 15:13:32; Parameter PMT Volts = 640; Parameter Scan Date = 2005-05-24; Parameter Pixel Size = 10; Parameter Laser on time = 212547; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 676 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54505.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.97; Parameter Scan Time = 11:59:32; Parameter PMT Volts = 580; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 179623; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.58; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.97; Parameter Scan Time = 11:59:32; Parameter PMT Volts = 610; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 544427; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.58; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 678 Barrett's(L)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54514.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 6720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.21; Parameter Scan Time = 11:22:22; Parameter PMT Volts = 640; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 173880; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.21; Parameter Scan Time = 11:22:22; Parameter PMT Volts = 660; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 538684; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: Expression data of CCMS_11

description: MSS, proximal

scan_protocol: standard Affymetrix procedures


title: NGM versus CeMM growth #2

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33638.gif


title: 671Barrett's (L)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54488.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.59; Parameter Scan Time = 13:23:39; Parameter PMT Volts = 560; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 178846; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.59; Parameter Scan Time = 13:23:39; Parameter PMT Volts = 630; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 543650; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 669 Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54498.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.01; Parameter Scan Time = 11:11:57; Parameter PMT Volts = 620; Parameter Scan Date = 2004-07-27; Parameter Pixel Size = 10; Parameter Laser on time = 178208; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.01; Parameter Scan Time = 11:11:57; Parameter PMT Volts = 610; Parameter Scan Date = 2004-07-27; Parameter Pixel Size = 10; Parameter Laser on time = 543012; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: T-5 AdenoCa

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61462.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.82; Parameter Scan Time = 11:09:02; Parameter PMT Volts = 580; Parameter Scan Date = 2005-05-21; Parameter Pixel Size = 10; Parameter Laser on time = 217747; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.82; Parameter Scan Time = 11:09:02; Parameter PMT Volts = 640; Parameter Scan Date = 2005-05-21; Parameter Pixel Size = 10; Parameter Laser on time = 582551; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 683 Barrett's (S)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54484.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 6400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.22; Parameter Scan Time = 12:28:06; Parameter PMT Volts = 580; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 178790; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.22; Parameter Scan Time = 12:28:06; Parameter PMT Volts = 640; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 543594; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.98; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: N-6 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61463.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.18; Parameter Scan Time = 11:25:02; Parameter PMT Volts = 620; Parameter Scan Date = 2005-05-21; Parameter Pixel Size = 10; Parameter Laser on time = 217763; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.18; Parameter Scan Time = 11:25:02; Parameter PMT Volts = 670; Parameter Scan Date = 2005-05-21; Parameter Pixel Size = 10; Parameter Laser on time = 582567; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 679 Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54510.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 6520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.63; Parameter Scan Time = 12:29:12; Parameter PMT Volts = 620; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 173946; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.63; Parameter Scan Time = 12:29:12; Parameter PMT Volts = 860; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 538750; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.06; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: NGM versus CeMM growth #1

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33635.gif


title: 683 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54483.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.15; Parameter Scan Time = 12:14:01; Parameter PMT Volts = 600; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 178776; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.15; Parameter Scan Time = 12:14:01; Parameter PMT Volts = 640; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 543579; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 675 Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54482.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.69; Parameter Scan Time = 14:18:39; Parameter PMT Volts = 540; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 179762; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.69; Parameter Scan Time = 14:18:39; Parameter PMT Volts = 800; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 544565; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.66; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 671 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54487.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5960; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.50; Parameter Scan Time = 13:08:48; Parameter PMT Volts = 600; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 178830; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.50; Parameter Scan Time = 13:08:48; Parameter PMT Volts = 630; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 543634; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 675 Barrett's(L)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54481.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 7000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.37; Parameter Scan Time = 13:01:58; Parameter PMT Volts = 580; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 179686; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.37; Parameter Scan Time = 13:01:58; Parameter PMT Volts = 580; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 544490; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.62; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 673 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54511.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.60; Parameter Scan Time = 14:40:35; Parameter PMT Volts = 580; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 173639; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.60; Parameter Scan Time = 14:40:35; Parameter PMT Volts = 860; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 538443; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao