title: Eker Kidney C d14 biological rep3	 48

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control OTA_d14_biological replicate3


title: Eker Kidney C d3 biological rep3	 42

status: Public on Aug 23 2007

type: RNA

city: Konstanz

first: Daniel

middle: R.

last: Dietrich

address: Jakob-Burckhardt-Str. 25

department: Environmental Toxicology

country: Germany

institute: University of Konstanz

description: total RNA from kidney cortex and outer medulla

hyb_protocol: According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays , and hybridized cRNA

scan_protocol: The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)

data_processing: Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control OTA_d3_biological replicate 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Affymetrix, USA; GeneChip® Expression Analysis, GeneChip sample Cleanup Module, 701194 Rev.1)

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Midi Kit (Qiagen, Cat No. 75144)

treatment_protocol: Daily gavaged with 0,1M sodium bicarbonate. After 3 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.

tag: Genotype

value: Eker

tag: Gender

value: male

tag: Age

value: 10-14 weeks


title: Eker Kidney C d1 biological rep1	 37

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control_d1_biological replicate 1

treatment_protocol: Once Gavaged with in 0,1M sodium bicarbonate. 24h later: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: Eker Kidney C d1 biological rep3	 39

source_name: Kidney cortex and outer medulla_Eker_vehicle control_OTA d1_biological replicate 3


title: O26 no.4 (strain 12719) replicate 2

type: genomic

city: Kiyotake

first: Yoshitoshi

last: Ogura

state: Miyazaki

address: Kihara 5200

department: Frontier science reserch center

country: Japan

institute: University of Miyazaki

hyb_protocol: The Cy5-labeled and the Cy3-labeled DNA preparations (15 µl for each) were mixed with a 90-µl hybridization solution containing 6.4 x SSC, 0.64 % sodium dodecyl sulfate (SDS), and 1.3 mg/ml  yeast tRNA.  After incubation at 96ºC for 2 min, the denatured sample was applied to a microarray slide and incubated on an ArrayBooster hybridization apparatus (Advalytix AG, Brunnthal, Germany) at 50ºC for 16 h.  The slide was then washed twice in 2x SSC/0.2% SDS at room temperature for 10 min, twice in 0.2x SSC/0.2% SDS at 50ºC for 5 min, and twice in 0.2x SSC at room temperature for 10 min.  Finally, the slide was briefly rinsed with ethanol and dried by centrifugation.

scan_protocol: Scanned with a FLA-8000 scanner (Fuji Photofilm, Tokyo, Japan).  The obtained data were analyzed by the ArrayVision 8.0 software (Imaging Research).

data_processing: Spots with reference signal intensities lower than the local background (LBG)  plus 5 standard deviations or with some spotting abnormalities were removed from analysis. Signal intensities of other spots were corrected by subtracting the LBG.

molecule: genomic DNA

organism: Escherichia coli

source_name: Genomic DNA from O26 strain 12719

label_protocol: First, 3 µg of genomic DNA was labeled with aminoallyl-modified dUTP (Sigma) using the Bioprime DNA Labeling System (Invitrogen).  DNAs were not sheared or digested by restriction enzymes prior to the labeling.  The aminoallyl-labeled DNA was purified by Microcon YM-30 (Millipore), dried in a speed-vac, and resuspended in 10 µl of 50 mM NaHCO3.  After adding 10 µl of dimethyl sulfoxide solution containing Cy3 or Cy5 monofunctional reactive dye (Amersham), the sample was incubated at room temperature in the dark for 1 h to allow the dye to couple with DNA.  The fluorescently labeled DNA was finally purified by the Qiaquick PCR purification kit (Qiagen) into 30 µl elution buffer provided by the manufacturer.

growth_protocol: Cells were grown to the stationary phase at 37ºC in Luria-Bertani medium.

extract_protocol: Genomic DNA was purified using the Genomic-tip 100/G and Genomic DNA buffer set (Qiagen) according to the manufacturer's instruction.

tag: Enteroheamorragic E. coli

source_name: O157 strain Sakai


title: O26 no.8 (strain ED411) replicate 2

source_name: Genomic DNA from O26 strain ED411


title: Eker Kidney C d7 biological rep1	 43

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control OTA_d7_biological replicate 1

treatment_protocol: Daily gavaged with 0,1M sodium bicarbonate. After 7 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: O26 no.4 (strain 12719) replicate 1


title: Eker Kidney C d1 biological rep2	 38

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control OTA_d1_biological replicate 2


title: Eker Kidney OTA d7 biological rep1	 31

source_name: Kidney cortex and outer medulla_Eker_OTA treated_d7_biological replicate 1

treatment_protocol: Daily gavaged with OTA (210µg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 7 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater


title: Eker Kidney OTA d14 biological rep2	 35

source_name: Kidney cortex and outer medulla_Eker_OTA treated_d14_biological replicate2

treatment_protocol: Daily gavaged with OTA (210µg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 14 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlate


title: O26 no.3 (strain 11656) replicate 1

source_name: Genomic DNA from O26 strain 11656


title: Eker Kidney OTA d3 biological rep3	 30

source_name: Kidney cortex and outer medulla_Eker_OTA treated_d3_biological replicate 2

treatment_protocol: Daily gavaged with OTA (210µg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 3 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater


title: Eker Kidney OTA d14 biological rep1	 34

source_name: Kidney cortex and outer medulla_Eker_OTA treated_d14_biological replicate1


title: Eker Kidney OTA d14 biological rep3	 36

source_name: Kidney cortex and outer medulla_Eker_OTA treated_d14_biological replicate3


title: Eker Kidney OTA d3 biological rep1	 28

source_name: Kidney cortex and outer medulla_Eker_OTA treated_d3_biological replicate 1


title: O26 no.2 (strain 11368) replicate 2

source_name: Genomic DNA from O26 strain 11368


title: Eker Kidney OTA d7 biological rep2	 32

source_name: Kidney cortex and outer medulla_Eker_OTA treated_d7_biological replicate 2


title: O26 no.1 (strain 11044) replicate 1

source_name: Genomic DNA from O26 strain 11044


title: Eker Kidney C d14 biological rep1	 22

hyb_protocol: According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays , and hybridized cRNA was stained using Phycoerythrin-conjugated Streptavidin

data_processing: Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity of 100.

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control (AA)_d14_biological replicate1

treatment_protocol: Daily gavaged with 0,1M sodium bicarbonate. After 14 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: Eker Kidney OTA d1 biological rep2	 26

description: total RNA from kindey cortex and outer medulla

source_name: Kidney cortex and outer medulla_Eker_OTA treated_d1_biological replicate 2

treatment_protocol: Gavaged with one single dose OTA (210µg_ kg BW), dissolved in 0,1M sodium bicarbonate. 24h later: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in


title: Eker Kidney OTA d1 biological rep3	 27

source_name: Kidney cortex and outer medulla_Eker_OTA treated_d1_biological replicate 3


title: O26 no.2 (strain 11368) replicate 1

source_name: O157 strain Sakai


title: Eker Kidney C d14 biological rep2	 23

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control (AA)_d14_biological replicate2


title: O26 no.1 (strain 11044) replicate 2


title: Eker Kidney C d7 biological rep3	 21

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control (AA)_d7_biological replicate 3


title: Eker Kidney C d7 biological rep2	 20

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control (AA)_d7_biological replicate 2


title: Eker Kidney C d14 biological rep3	 24

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control (AA)_d14_biological replicate3


title: Wild type Kidney AA d3 biological rep3	 54

source_name: Kidney cortex and outer medulla_wild type_AA treated_d3_biological replicate 2

treatment_protocol: Daily gavaged with AA (10mg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 3 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.

value: wild type


title: Eker Kidney OTA d1 biological rep1	 25

source_name: Kidney cortex and outer medulla_Eker_OTA treated_d1_biological replicate 1


title: Eker Kidney C d3 biological rep2	 17

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control (AA treatement)_biological replicate 2


title: Eker Kidney C d3 biological rep1	 16

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control (AA treatement)_d3_biological replicate 1


title: O157 no.8 (strain 982243) replicate 2

source_name: Genomic DNA from O157 strain 982243


title: O157 no.9 (strain 981795) replicate 1

source_name: Genomic DNA from O157 strain 981795


title: O157 no.9 (strain 981795) replicate 2


title: Eker Kidney C d3 biological rep3	 18

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control (AA)_d3_biological replicate 2


title: O157 no.8 (strain 982243) replicate 1


title: O157 no.7 (strain 981456) replicate 1

source_name: Genomic DNA from O157 strain 981456


title: Eker Kidney C d7 biological rep1	 19

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control (AA)_d7_biological replicate 1


title: O157 no.6 (strain 990570) replicate 1

source_name: Genomic DNA from O157 strain 990570


title: Eker Kidney AA d14 biological rep3	 12

source_name: Kidney cortex and outer medulla_Eker_AA treated_d14_biological replicate3

treatment_protocol: Daily gavaged with AA (10mg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 14 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: O157 no.6 (strain 990570) replicate 2


title: O157 no.7 (strain 981456) replicate 2


title: Eker Kidney AA d14 biological rep1	 10

source_name: Kidney cortex and outer medulla_Eker_AA treated_d14_biological replicate1


title: O157 no.5 (strain 980551) replicate 2

source_name: Genomic DNA from O157 strain 980551

source_name: O157 strain Sakai


title: Eker Kidney AA d14 biological rep2	 11

source_name: Kidney cortex and outer medulla_Eker_AA treated_d14_biological replicate2


title: RAG H3K4me3 ID92002a

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohr-Gasse 7

country: Austria

institute: Research Institute of Molecular Pathology

description: Chip-chip Rag2-/- pro-B cells H3K4me3

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

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

data_processing: log2(Signal Cy5/Signal Cy3) - tukey.biweight(Signal Cy5/Signal Cy3)

organism: Mus musculus

source_name: H3K4me3 ChIP DNA from H3K9ac ChIP DNA from Rag2-/- pro-B cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Rag2-/- pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells.

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: Rag2-/- pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice.

value: 5 days in culture

tag: Tissue

value: pro-B cells

tag: Strain

tag: Antibody

tag: Type

value: ChIP

source_name: Input DNA from Rag2-/- pro-B cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: see chanel 1

extract_protocol: see chanel 1

treatment_protocol: see chanel 1

value: Input


title: O157 no.5 (strain 980551) replicate 1


title: Eker Kidney C d1 biological rep2	 14

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control (AA treatement)_d1_biological replicate 2


title: P5R2 H3K4me3 ID91992a

description: Chip-chip Pax5-/-Rag2-/- pro-B cells H3K4me3

source_name: H3K4me3 ChIP DNA from Pax5-/- Rag2-/- pro-B cells

growth_protocol: Pax5-/- Rag2-/- pro-B cells were cultured on gamma-irradiated ST2 cells in IL-7 containing IMDM medium.

treatment_protocol: Pax5-/- Rag2-/- pro-B cells are an established cell line.

value: cell line

source_name: Input DNA from Pax5-/- Rag2-/- pro-B cells


title: Eker Kidney AA d7 biological rep2	 8

source_name: Kidney cortex and outer medulla_Eker_AA treated_d7_biological replicate 2

treatment_protocol: Daily gavaged with AA (10mg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 7 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: O157 no.4 (strain 990281) replicate 2

source_name: Genomic DNA from O157 strain 990281


title: Eker Kidney AA d3 biological rep3	 6

source_name: Kidney cortex and outer medulla_Eker_AA treated_d3_biological replicate 2


title: O26 no.5 (strain 12929) replicate 1

source_name: Genomic DNA from O26 strain 12929


title: Eker Kidney AA d7 biological rep1	 7

source_name: Kidney cortex and outer medulla_Eker_AA treated_d7_biological replicate 1


title: Eker Kidney C d1 biological rep1	 13

source_name: Kidney cortex and outer medulla_Eker_time mached vehicle control (AA treatement)_d1_biological replicate 1


title: Eker Kidney AA d7 biological rep3	 9

source_name: Kidney cortex and outer medulla_Eker_AA treated_d7_biological replicate 3


title: Eker Kidney C d1 biological rep3	 15

source_name: Kidney cortex and outer medulla_Eker_vehicle control_(AA treatement) d1_biological replicate 3


title: O157 no.3 (strain 980706) replicate 2

source_name: Genomic DNA from O157 strain 980706


title: RAG H3K9ac ID95879a

description: Chip-chip Rag2-/- pro-B cells H3K9ac

source_name: H3K9ac ChIP DNA from Rag2-/- pro-B cells

source_name: Input DNA from Rag2-/- pre-B cells


title: RAG H3K9ac ID87920a

description: Chip-chip Pax5-/-Rag2-/- pro-B cells H3K9ac

source_name: H3K9ac ChIP DNA from Pax5-/- Rag2-/- pro-B cells


title: P5R2 H3K4me2 ID96063a

description: Chip-chip Pax5-/-Rag2-/- pro-B cells H3K4me2

source_name: H3K4me2 ChIP DNA from Pax5-/- Rag2-/- pro-B cells


title: RAG H3K4me2 ID95879a

description: Chip-chip Rag2-/- pro-B cells H3K4me2

source_name: H3K4me2 ChIP DNA from Rag2-/- pro-B cells


title: Eker Kidney AA d3 biological rep1	 4

source_name: Kidney cortex and outer medulla_Eker_AA treated_d3_biological replicate 1


title: O157 no.2 (strain 980938) replicate 1

source_name: Genomic DNA from O157 strain 980938

source_name: O157 strain Sakai


title: O157 no.2 (strain 980938) replicate 2


title: Eker Kidney AA d1 biological rep1	 1

source_name: Kidney cortex and outer medulla_Eker_AA treated_d1_biological replicate 1

treatment_protocol: Gavaged with one single dose AA (10mg_ kg BW), dissolved in 0,1M sodium bicarbonate. 24h later: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater.


title: O157 no.3 (strain 980706) replicate 1


title: O157 no.4 (strain 990281) replicate 1

source_name: Genomic DNA from O157 strain 990281


title: Eker Kidney AA d1 biological rep3	 3

source_name: Kidney cortex and outer medulla_Eker_AA treated_d1_biological replicate 3


title: Eker Kidney AA d3 biological rep2	 5

source_name: Kidney cortex and outer medulla_Eker_AA treated_d3_biological replicate 2


title: Eker Kidney AA d1 biological rep2	 2

source_name: Kidney cortex and outer medulla_Eker_AA treated_d1_biological replicate 2


title: Schizosaccharomyces pombe h- sax2- cyr1- cells mating pheromone P-factor 4hr treatment

status: Public on Aug 22 2007

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

description: Schizosaccharomyces pombe h- sax2- cyr1- cells treated with mating pheromone P-factor for 4 hours compared to non-treated sample.

hyb_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

scan_protocol: Slides were scanned using Bio-rad Vers-Array ChipReader.

data_processing: Scanned slides were quantified with Imagene 4.2 software. Quantified data were loaded to GeneSpring software and normalized by lowess normalization.

organism: Schizosaccharomyces pombe

growth_protocol: Cells were grown at 30° C in MSL to a density of 2 x 106 cells/ml, and chemically synthesized P-factor (made by Alto Bioscience, Birmingham, UK) was added to a final concentration of 1 μg/ml. Samples were taken for RNA preparation after 4 hours.

treatment_protocol: Schizosaccharomyces pombe h- sax2- cyr1- cells treated with mating pheromone P-factor for 4 hours.

source_name: Schizosaccharomyces pombe h- sax2- cyr1- cells mating pheromone P-factor non-treated control.

growth_protocol: Cells were grown at 30° C in MSL to a density of 2 x 106 cells/ml without chemical added as control.

treatment_protocol: Schizosaccharomyces pombe h- sax2- cyr1- cells mating pheromone P-factor non-treated.


title: Eker Kidney OTA d7 biological rep3	 33

source_name: Kidney cortex and outer medulla_Eker_OTA treated_d7_biological replicate 3


title: Schizosaccharomyces pombe h+ cyr1- cells mating pheromone M-factor 4hr treatment

description: Schizosaccharomyces pombe h+ cyr1- cells treated with mating pheromone M-factor for 4 hours compared to non-treated sample.

label_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

growth_protocol: Cells were grown at 30° C in MSL to a density of 2 x 106 cells/ml, and chemically synthesized M-factor (made by Schafer-N, Copenhagen, Denmark) was added to a final concentration of 1 μg/ml. Samples were taken for RNA preparation after 4 hours.

treatment_protocol: Schizosaccharomyces pombe h+ cyr-1  cells treated with mating pheromone M-factor for 4 hours.

treatment_protocol: Schizosaccharomyces pombe h+ cyr1- cells mating pheromone M-factor non-treated.

tag: Schizosaccharomyces pombe h+ cyr1- cells mating pheromone M-factor non-treated control.


title: 8 month old hurpin transgenic mouse, male 17 Transgene

status: Public on Aug 18 2007

city: Duesseldorf

first: Birgit

last: Andree

address: Moorenstr. 5

institute: BMFZ

description: Everything done according Affymetrix protocols

data_processing: MAS 5.0

label: GeneChip® One-Cycle Target Labeling

source_name: skin of belly


title: 8 month old wildtype mouse, male 26 Wildtype

tag: 8 month old wildtype mouse, male


title: S. pombe h- sax2- cyr-  cells mating pheromone P-factor treatment compared to h+ cyr1- cells M-factor treatement

description: Schizosaccharomyces pombe h- sax2- cyr-  cells 6 hours treatment with mating pheromone P-factor compared to h+ cyr1- cells 6 hours treatment with  M-factor.

source_name: Schizosaccharomyces pombe h- sax2- cyr-  cells mating pheromone P-factor treatment

growth_protocol: Cells were grown at 30° C in MSL to a density of 2 x 106 cells/ml, and chemically synthesized or P-factor (made by Alto Bioscience, Birmingham, UK) was added to a final concentration of 1 μg/ml. Samples were taken for RNA preparation after 6 hours.

extract_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

treatment_protocol: S. pombe h- sax2- cyr-  cells treated with mating pheromone P-factor for 6 hours.

source_name: Schizosaccharomyces pombe h+ cyr1- cells mating pheromone M-factor treatement

growth_protocol: Cells were grown at 30° C in MSL to a density of 2 x 106 cells/ml, and chemically synthesized M-factor (made by Schafer-N, Copenhagen, Denmark) was added to a final concentration of 1 μg/ml. Samples were taken for RNA preparation after 6 hours.

treatment_protocol: Schizosaccharomyces pombe h+ cyr1- cells treated with mating pheromone M-factor for 6 hours.


title: 8 month old wildtype mouse, female 29 b Wildtype

tag: 8 month old wildtype mouse, female


title: 8 month old hurpin transgenic mouse, female 7 Transgene


title: Schizosaccharomyces pombe h- sax2- cyr1- cells mating pheromone P-factor 2hr treatment

description: Schizosaccharomyces pombe h- sax2- cyr1- cells treated with mating pheromone P-factor for 2 hours compared to non-treated sample.

growth_protocol: Cells were grown at 30° C in MSL to a density of 2 x 106 cells/ml, and chemically synthesized P-factor (made by Alto Bioscience, Birmingham, UK) was added to a final concentration of 1 μg/ml. Samples were taken for RNA preparation after 2 hours.

treatment_protocol: Schizosaccharomyces pombe h- sax2- cyr1- cells treated with mating pheromone P-factor for 2 hours.

treatment_protocol: chizosaccharomyces pombe h- sax2- cyr1- cells mating pheromone P-factor non-treated.

tag: chizosaccharomyces pombe h- sax2- cyr1- cells mating pheromone P-factor non-treated control.


title: Schizosaccharomyces pombe h+ cyr1- cells mating pheromone M-factor 2hr treatment

description: Schizosaccharomyces pombe h+ cyr1-  cells treated with mating phermone M-factor for 2 hours compared to non-treated sample.

growth_protocol: Cells were grown at 30° C in MSL to a density of 2 x 106 cells/ml, and chemically synthesized M-factor (made by Schafer-N, Copenhagen, Denmark) was added to a final concentration of 1 μg/ml. Samples were taken for RNA preparation after 2 hours.

treatment_protocol: Schizosaccharomyces pombe  h+ cyr1- cells treatd with mating pheromone M-factor for 2 hours.

treatment_protocol: Schizosaccharomyces pombe h+ cyr1- cells non-treated control.


title: 8 month old hurpin transgenic mouse, female 84 Transgene


title: 13185_methylatedDNA_peripheralBlood

status: Public on Aug 21 2007

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

country: USA

institute: UT MD Anderson Cancer Center

description: The goal of the experiment – genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters

hyb_protocol: we used Agilent microarray protocols for hybridization, blocking and washing (details can be found at www.agilent.com).  Briefly,labeled samples were hybridized to arrays in the presence of human Cot-1 DNA for 40 hr at 65°C. The arrays were washed by Agilent Oligo aCGH wash buffer 1 for 5 mins, wash buffer 2 for 1 min, Acetonitrile for 1 min, and Stabilization and drying solution for 30s.

scan_protocol: we used Agilent scanner and feature extraction software for data process.

data_processing:
normalization using LOWESS method.
The LogRatio was calculated based on:
If red channel signal is positive and significant vs background and greater than red background SD (R) and green channel signal is positive and significant vs background and greater than green background SD (G), then the ratio is R/G, and feature extraction uses the dye-normalized signals for both channels for the calculations.
If red channel signal is not positive and significant vs background or less than red background SD (r) and green channel signal is Positive and significant vs background and greater than green background SD (G), then ratio is  r/G, and feature extraction uses the dye-normalized green signal and the dye-normalized red background SD signal (surrogate) for the calculations.
If red channel signal is not positive and significant vs background or less than red background SD (R), and green channel signal is not positive and significant vs background or less than green background SD (g), then ratio is r/g and feature extraction uses surrogates for both channels, and sets the log ratio=0, set the p-value=1.
If red channel signal is positive and significant vs background and greater then red background SD (R), and green channel signal is not positive and significant vs background or less than green background SD (g), then ratio is R/g, and feature extraction uses the dye-normalized red signal and the dye-normalized red signal and the dye-normalized green background SD signal (surrogate) for the calculations.
Gene selection procedure:
Probe sequences were downloaded from the Agilent website at www.agilent.com.  Each probe was BLASTed against all sequences in the SmaI/XmaI database using BLAST v2.2.8 downloaded from NCBI (/data/bioinfo/SequenceTools/blast/).  Probes with multiple BLAT hits were excluded from further study.  Probes residing in SmaI/XmaI fragments were identified with the annotation for fragment length, status of CGI and repetitive sequences.  The signal intensity for the probes within the SmaI/XmaI fragments was adjusted for background and analyzed for the ratio between Cy3 and Cy5 signals.  All data analysis (sensitivity and reproducibility, correlation between methylation level and chromosome location, CGI, and repetitive sequences) were carried out in Excel (Microsoft).  The resulting data sets are accessible in the supplementary database.  We used the following criteria to select hypermethylated probes in PBL (Cy3) relative to fully methylated DNA (Cy5): signal intensity of Cy3>3 times background and ratio of Cy3/Cy5>=1.5.  We performed bisulfite-pyrosequencing on 38 randomly selected genes showing higher signal intensity in PBL, and determined that these criteria most accurately identified hypermethylated loci.

organism: Homo sapiens

source_name: Normal peripheral blood

label_protocol: using random primer direct labeling by Bioprimer CGH labeling kit from Invitrogen (Cat. No. 18095-011)

extract_protocol: standard phenol-chloroform extraction

source_name: in vitro methylated DNA

tag: Normal peripheral blood is from a healthy donor, female, 35 yrs old; treated with SSSI methylase


title: 8 month old wildtype mouse, male 28 Wildtype


title: Schizosaccharomyces pombe h+ cyr1- cells mating pheromone M-factor 6hr treatment

description: Schizosaccharomyces pombe h+ cyr1- cells treated with mating pheromone M-factor for 6 hours compared to non-treated sample.

tag: Schizosaccharomyces pombe h+ cyr1- cells treated with mating pheromone M-factor for 6 hours.

source_name: Schizosaccharomyces pombe h+ cyr1- cells non-treated control

treatment_protocol: Schizosaccharomyces pombe h+ cyr1-  strain non-treated control.


title: Schizosaccharomyces pombe h- sax2- cyr- h- cells compared to h+ cyr1- cells, non-treated

source_name: Schizosaccharomyces pombe h- sax2- cyr- h- cells, non-treated

growth_protocol: Cells were grown at 30° C in MSL to a density of 2 x 106 cells/ml without chemical added. sample is taken for RNA extraction.

source_name: SchizSchizosaccharomyces pombe h+ cyr1- cells, non-treated


title: 13186_methylatedDNA_peripheralBlood

tag: Normal peripheral blood is from a healthy donor, female, 35 yrs old

source_name: vitro methylated DNA


title: Schizosaccharomyces pombe h- sax2- cyr1- cells mating pheromone P-factor 6hr treatment

description: Schizosaccharomyces pombe h- sax2- cyr1- cells treated with mating pheromone P-factor for 6 hours compared to non-treated sample.

growth_protocol: Cells were grown at 30° C in MSL to a density of 2 x 106 cells/ml, and chemically synthesized P-factor (made by Alto Bioscience, Birmingham, UK) was added to a final concentration of 1 μg/ml. Samples were taken for RNA preparation after 6 hours.

treatment_protocol: Schizosaccharomyces pombe h- sax2- cyr1- cells treated with mating pheromone P-factor for 6 hours.

tag: Schizosaccharomyces pombe h- sax2- cyr1- cells mating pheromone P-factor non-treated control.


title: 13903_methylatedDNA_peripheralBlood

tag: Normal peripheral blood is from a healthy donor, female, 35 yrs old, treated with SSSI methylase


title: 8 month old hurpin transgenic mouse, male 11 Transgene


title: 8 month old wildtype mouse, female 29 Wildtype


title: O26 no.3 (strain 11656) replicate 2

source_name: Genomic DNA from O26 strain 11656

source_name: O157 strain Sakai


title: Eker Kidney OTA d3 biological rep2	 29

source_name: Kidney cortex and outer medulla_Eker_OTA treated_d3_biological replicate 2

treatment_protocol: Daily gavaged with OTA (210µg_ kg BW), dissolved in 0,1M sodium bicarbonate. After 3 days: Anesthesia with pentobarbital, exsanguination subsequent to retrograde perfusion with PBS. Kidney collection and storage in RNAlater

tag: Genotype


title: 13902_methylatedDNA_peripheralBlood

source_name: normal peripheral blood


title: 21D S2 TC 5/3/02

status: Public on Aug 17 2007

city: Stockholm

first: Annika

last: Saaf

department: Department of Molecular Medicine & Surgery

institute: Karolinska Institute, Karolinska University Hospital, Solna

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34922.gif

hyb_protocol: not provided

scan_protocol: not provided

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)

source_name: Stratagene amp reference 7/30/02

label_protocol: not provided

extract_protocol: not provided

tag: Stratagene amp reference 7/30/02

tag: Time


title: 14D S1 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33832.gif

source_name: stratagene ref aRNA 7/30/02

tag: stratagene ref aRNA 7/30/02


title: 26D S1 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33817.gif


title: 1D S3_5b

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37236.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 7240; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf 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 = 30.08; Parameter Scan Time = 10:47:21; Parameter PMT Volts = 590; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 43464; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.80; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf 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 = 30.08; Parameter Scan Time = 10:47:21; Parameter PMT Volts = 620; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 262459; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.28; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf

source_name: Stratagene Human amp reference 7/30/02

tag: Stratagene Human amp reference 7/30/02

value: 1 d


title: 21D S1 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33833.gif


title: 12am S3_2b (amp4)

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37160.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1600, 7400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf 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 = 29.87; Parameter Scan Time = 10:17:17; Parameter PMT Volts = 580; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 43433; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.82; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf 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 = 29.87; Parameter Scan Time = 10:17:17; Parameter PMT Volts = 610; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 262428; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.26; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf

value: 0 h


title: 1D S3_5a

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37235.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1600, 7400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf 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 = 29.99; Parameter Scan Time = 10:32:24; Parameter PMT Volts = 580; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 43449; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.74; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf 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 = 29.99; Parameter Scan Time = 10:32:24; Parameter PMT Volts = 610; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 262444; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.28; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: 1D S1 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33816.gif


title: 7D S2 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34509.gif

source_name: Staratagene amp reference 7/30/02

tag: Staratagene amp reference 7/30/02

value: 7 d


title: 8PM BF

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32564.gif

value: 8 h


title: HKCO30N

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46488.gif
Disease State: Healthy Normal Colon sample

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 580, 4940; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 30.51; Parameter Scan Time = 22:27:11; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 133614; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.69; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 30.51; Parameter Scan Time = 22:27:11; Parameter PMT Volts = 700; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 352585; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.92; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified CRH

tag: amplified CRH

source_name: amplified, HKCO30N

label_protocol: Fluorescently labeled cDNA prepared from RNA linearly amplified using MessageAmp (Ambion) was hybridized to the array in a two-color comparative format, with normal colon or colon cancer samples labeled with Cy-5, and a reference pool of human mRNAs labelled with Cy-3 (Stratagene, Cat #740000).

tag: amplified, HKCO30N


title: 3 PM BF

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32563.gif

value: 3 h


title: 2D S1 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33831.gif

value: 2 d


title: HKCO60N

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46490.gif
Disease State: Healthy Normal Colon sample

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 310, 4790; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 30.72; Parameter Scan Time = 22:49:27; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 133637; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.78; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 30.72; Parameter Scan Time = 22:49:27; Parameter PMT Volts = 680; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 352607; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.94; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified, HKCO60N

tag: amplified, HKCO60N


title: 4D S2 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34508.gif

source_name: Stratagene amplified reference 7/30/02

tag: Stratagene amplified reference 7/30/02

value: 4 d


title: HKCO05N

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Non-tumor tissue, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46388.gif
Disease State: Healthy Normal Colon sample

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 5960; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 30.26; Parameter Scan Time = 22:39:41; Parameter PMT Volts = 610; Parameter Scan Date = 2003-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 132666; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 30.26; Parameter Scan Time = 22:39:41; Parameter PMT Volts = 730; Parameter Scan Date = 2003-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 351637; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.89; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified, HKCO05N

tag: amplified, HKCO05N


title: HKCO22T

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46496.gif
Disease State: Tumor Colon Samples

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 530, 6130; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 31.00; Parameter Scan Time = 00:10:36; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 133718; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.33; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 31.00; Parameter Scan Time = 00:10:36; Parameter PMT Volts = 680; Parameter Scan Date = 2003-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 352689; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.95; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified, HKCO22T

tag: amplified, HKCO22T


title: HKCO13N

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46489.gif
Disease State: Healthy Normal Colon sample

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 580, 4940; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 30.63; Parameter Scan Time = 22:38:17; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 133625; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 30.63; Parameter Scan Time = 22:38:17; Parameter PMT Volts = 680; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 352596; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.93; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified, HKCO13N

tag: amplified, HKCO13N


title: 10D S1 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33810.gif


title: HKCO61T

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46459.gif
Disease State: Tumor Colon Samples

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1060, 5650; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 31.82; Parameter Scan Time = 23:49:26; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 133021; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.97; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 31.82; Parameter Scan Time = 23:49:26; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 351992; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.94; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified, HKCO61T

tag: amplified, HKCO61T


title: HKCO24N

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46486.gif
Disease State: Healthy Normal Colon sample

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 5720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 30.20; Parameter Scan Time = 22:03:59; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 133592; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 30.20; Parameter Scan Time = 22:03:59; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 352562; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.92; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified, HKCO24N

tag: amplified, HKCO24N


title: HKCO31T

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46541.gif
Disease State: Tumor Colon Samples

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 240, 5000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 30.75; Parameter Scan Time = 22:14:36; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 133821; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.86; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 30.75; Parameter Scan Time = 22:14:36; Parameter PMT Volts = 680; Parameter Scan Date = 2003-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 352791; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.92; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified, HKCO31T

tag: amplified, HKCO31T


title: HKCO25N

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46487.gif
Disease State: Healthy Normal Colon sample

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 580, 4940; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 30.36; Parameter Scan Time = 22:15:32; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 133603; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 30.36; Parameter Scan Time = 22:15:32; Parameter PMT Volts = 670; Parameter Scan Date = 2003-11-06; Parameter Pixel Size = 10; Parameter Laser on time = 352574; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.92; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified, HKCO25N

tag: amplified, HKCO25N


title: 2D BF

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32565.gif


title: 21D BF

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32566.gif


title: PD S3_amp22

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36867.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1920, 8000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf 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 = 29.71; Parameter Scan Time = 10:57:44; Parameter PMT Volts = 560; Parameter Scan Date = 2002-12-11; Parameter Pixel Size = 10; Parameter Laser on time = 44250; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.74; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf 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 = 29.71; Parameter Scan Time = 10:57:44; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-11; Parameter Pixel Size = 10; Parameter Laser on time = 263245; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.22; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf

source_name: PD S3_amp22

tag: PD S3_amp22


title: HKCO59T

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46457.gif
Disease State: Tumor Colon Samples

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1060, 5650; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 31.64; Parameter Scan Time = 23:27:20; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 133000; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 31.64; Parameter Scan Time = 23:27:20; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 351971; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.94; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified, HKCO59T

tag: amplified, HKCO59T


title: 14D BF

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32276.gif

tag: Time


title: 10D BF

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32275.gif

tag: stratagene ref aRNA 7/30/02


title: 4D S3_7a

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37032.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 7240; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf 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 = 30.20; Parameter Scan Time = 11:02:05; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 43478; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.71; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf 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 = 30.20; Parameter Scan Time = 11:02:05; Parameter PMT Volts = 650; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 262473; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.29; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf

tag: Stratagene Human amp reference 7/30/02


title: 7D BF

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32274.gif


title: 7D* S3_9f

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36866.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 7400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf 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 = 30.72; Parameter Scan Time = 12:27:08; Parameter PMT Volts = 580; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 43563; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.71; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf 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 = 30.72; Parameter Scan Time = 12:27:08; Parameter PMT Volts = 610; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 262558; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.31; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: 5D S3_8b

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36864.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 7320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf 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 = 30.57; Parameter Scan Time = 11:58:07; Parameter PMT Volts = 590; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 43534; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.71; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf 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 = 30.57; Parameter Scan Time = 11:58:07; Parameter PMT Volts = 620; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 262529; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.30; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf

value: 5 d


title: 1D BF

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32272.gif

scan_protocol: not provided


title: 7D* S3_9d

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36865.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 8000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf 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 = 30.69; Parameter Scan Time = 12:14:39; Parameter PMT Volts = 580; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 43551; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf 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 = 30.69; Parameter Scan Time = 12:14:39; Parameter PMT Volts = 610; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 262546; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.31; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: HKCO58T

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46456.gif
Disease State: Tumor Colon Samples

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 6070; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 31.61; Parameter Scan Time = 23:16:26; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 132989; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 31.61; Parameter Scan Time = 23:16:26; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 351959; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.93; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified, HKCO58T

tag: amplified, HKCO58T


title: 4D S3_7b

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36863.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 7240; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf 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 = 30.39; Parameter Scan Time = 11:19:51; Parameter PMT Volts = 610; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 43496; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.71; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf 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 = 30.39; Parameter Scan Time = 11:19:51; Parameter PMT Volts = 640; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 262491; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.29; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: 12AM BF

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32271.gif

source_name: stratagene ref aRNA 7/30/02

value: 0 d


title: 4D BF

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32273.gif


title: 7D S1 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33809.gif


title: 14D S3_13b

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37045.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1920, 7600; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf 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 = 29.62; Parameter Scan Time = 10:41:29; Parameter PMT Volts = 570; Parameter Scan Date = 2002-12-11; Parameter Pixel Size = 10; Parameter Laser on time = 44233; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.71; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf 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 = 29.62; Parameter Scan Time = 10:41:29; Parameter PMT Volts = 620; Parameter Scan Date = 2002-12-11; Parameter Pixel Size = 10; Parameter Laser on time = 263228; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.21; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf

source_name: Stratagene Human amp reference 7/30/02


title: 4D S1 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33808.gif


title: 21D S3_14b

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35777.gif

source_name: Stratagene amp Human reference 7/30/02

tag: Stratagene amp Human reference 7/30/02


title: 14D S2 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34919.gif

source_name: Stratagene amp reference 7/30/02

tag: Stratagene amp reference 7/30/02


title: 12AM S3_2b (amp3)

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36862.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 7720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf 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 = 29.78; Parameter Scan Time = 10:01:52; Parameter PMT Volts = 590; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 43418; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.80; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf 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 = 29.78; Parameter Scan Time = 10:01:52; Parameter PMT Volts = 610; Parameter Scan Date = 2002-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 262413; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.24; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: HKCO05T

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46783.gif
Disease State: Tumor Colon Samples

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 870, 4820; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 31.42; Parameter Scan Time = 23:52:34; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-11; Parameter Pixel Size = 10; Parameter Laser on time = 134546; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.30; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 31.42; Parameter Scan Time = 23:52:34; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-11; Parameter Pixel Size = 10; Parameter Laser on time = 353516; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.93; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified CRH

tag: amplified CRH

source_name: amplified HKCO05T

tag: amplified HKCO05T


title: 7D S3_9a

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37043.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1920, 8040; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf 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 = 29.44; Parameter Scan Time = 09:57:48; Parameter PMT Volts = 580; Parameter Scan Date = 2002-12-11; Parameter Pixel Size = 10; Parameter Laser on time = 44189; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.74; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf 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 = 29.44; Parameter Scan Time = 09:57:48; Parameter PMT Volts = 610; Parameter Scan Date = 2002-12-11; Parameter Pixel Size = 10; Parameter Laser on time = 263184; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.18; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: 8 PM S1 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33807.gif


title: HKCO04T

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46629.gif
Disease State: Tumor Colon Samples

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 850, 5040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 31.39; Parameter Scan Time = 23:41:07; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-11; Parameter Pixel Size = 10; Parameter Laser on time = 134534; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 31.39; Parameter Scan Time = 23:41:07; Parameter PMT Volts = 670; Parameter Scan Date = 2003-11-11; Parameter Pixel Size = 10; Parameter Laser on time = 353505; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.93; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified HKCO04T

tag: amplified HKCO04T


title: 12 AM S1 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33805.gif


title: 3 PM S1 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33806.gif


title: 12 am S2 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34917.gif


title: HKCO50T

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46675.gif
Disease State: Tumor Colon Samples

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 4870; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 30.90; Parameter Scan Time = 22:32:42; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 134831; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.32; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 30.90; Parameter Scan Time = 22:32:42; Parameter PMT Volts = 670; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 353802; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.92; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified HKCO50T

tag: amplified HKCO50T


title: Expt189 MCM262 vs W6G 3

status: Public on Aug 16 2007

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Genome comparison, Map Recombination Event
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64612.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 370, 27620; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller 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 = 40.66; Parameter Scan Time = 14:09:14; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-16; Parameter Pixel Size = 10; Parameter Laser on time = 55359; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller 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 = 40.66; Parameter Scan Time = 14:09:14; Parameter PMT Volts = 730; Parameter Scan Date = 2005-10-16; Parameter Pixel Size = 10; Parameter Laser on time = 201284; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.37; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller

organism: Vibrio cholerae


title: HKCO02N

description:
Colon tissue samples for DNA microarrays; Samples of tumor and normal colon mucosa were collected from colon cancer resection from Department of Surgery, Queen Mary Hospital University of Hong Kong. Tissue was frozen in liquid nitrogen within 30 min of resection. Nonneoplastic mucosa from colon was dissected free of muscle and histologically confirmed to be tumor free by frozen section. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) from each tissue sample and processed for microarray hybridization.; Protocol Type = Biological Sample; Performer: Xin,,Chen
Simple annotation: Primary tumor, Colon Cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46627.gif
Disease State: Healthy Normal Colon sample

scan_protocol: Array images were scanned by using an Axon Scanner 4000B, and data were analyzed by using GenePix 3.0 (Axon Instruments, Union City, CA). Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 850, 5040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Xin,,Chen 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 = 31.33; Parameter Scan Time = 23:19:25; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-11; Parameter Pixel Size = 10; Parameter Laser on time = 134512; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.17; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen 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 = 31.33; Parameter Scan Time = 23:19:25; Parameter PMT Volts = 680; Parameter Scan Date = 2003-11-11; Parameter Pixel Size = 10; Parameter Laser on time = 353483; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.93; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Xin,,Chen

source_name: amplified HKCO02N

tag: amplified HKCO02N


title: Expt189 MCM260 vs W6G 3

description:
Simple annotation: Genome comparison, Map Recombination Event
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64611.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 170, 28670; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller 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 = 40.62; Parameter Scan Time = 14:00:52; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-16; Parameter Pixel Size = 10; Parameter Laser on time = 55352; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller 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 = 40.62; Parameter Scan Time = 14:00:52; Parameter PMT Volts = 740; Parameter Scan Date = 2005-10-16; Parameter Pixel Size = 10; Parameter Laser on time = 201276; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.37; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller


title: 21D S3_14a

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35776.gif


title: 26D S2 TC 5/3/02

description:
Simple annotation: epithelial cells, Caco-2
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34859.gif