title: Halobacterium Oxygen1 L2H 01 min 1

description: high oxygen at shift from anaerobic to aerobic vs. reference

source_name: Halobacterium NRC-1, aerobic at shift

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested while rapidly shifting to high (~90-100%, 5uM) oxygen.

tag: cells at 50.0% oxygen in turbidostat


title: Halobacterium Oxygen1 L2H -1min dye swap 1

status: Public on Jul 31 2007

type: RNA

city: Seattle

first: Amy

middle: K

last: Schmid

state: WA

country: USA

institute: Institute for Systemsbiology

description: reference vs. low oxygen -1min pre-shift

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:286

label: Alexa 532

molecule: total RNA

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium NRC-1, reference

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

tag: Halobacterium NRC-1 in standard growth medium at 37C

label: Alexa 647

source_name: Halobacterium NRC-1, anaerobic 1 minute pre-shift

growth_protocol:
Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 grown at 225 rpm
Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested at 1 minute prior to rapidly shifting to high (~90-100%, 5uM) oxygen for 6 hours, then to low oxygen for 6 hr, and back to high oxygen for 30 min.

treatment_protocol: 10mL of cells were harvested from turbidostat, pelleted at 13,000rpm for 0.5 min, and snap-frozen in a dry-ice ethanol bath.  Samples were stored at -80C until RNA extraction

tag: cells at 0.5% oxygen in turbidostat


title: Halobacterium Oxygen1 H 20 min 1

description: high oxygen 20 minutes after shift vs. reference

source_name: Halobacterium NRC-1, aerobic 20 minutes after shift from low to high oxygen

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested 20 minutes after rapidly shifting to high (~90-100%, 5uM) oxygen.

tag: cells at 93.7% oxygen in turbidostat

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 grown at 225 rpm


title: Halobacterium Oxygen1 H 05 min 1

description: high oxygen 5 minutes after shift vs. reference

source_name: Halobacterium NRC-1, aerobic 5 minutes after shift from low to high oxygen

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested five minutes after rapidly shifting to high (~90-100%, 5uM) oxygen.

tag: cells at 92.2% oxygen in turbidostat


title: HMEC  ox-PAPC 40 mcg/ml  1432059026_F

status: Public on Jul 30 2007

city: Los Angeles

first: Leslie

last: Ingram-drake

state: CA

department: Medicine/MIMG/Human Genetics

institute: UCLA

description: Replicate of HMEC ox-PAPC 40 mcg/ml

data_processing: The data were analyzed with Illumina Inc. BeadStudio version 1.5.0.34 and normalized by rank invariant method.

label: Biotin Streptavidin-Cy3

organism: Homo sapiens

source_name: HMEC

tag: Confluent HMEC in 6-well plates were treated in triplicate by ox-PAPC 40 mcg/ml for 4 hours. Cells were harvested and cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity. Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/mcl, and then 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts. The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA. The microarray data was normalized and analyzed by Illumina Inc. BeadStudio software, version 1.5.0.34 (Illumina, Inc. San Diego, CA)


title: HMEC  ox-PAPC 40 mcg/ml  1432059026_H

description: Replicate of HMEC ox-PAPC 40 mcg/ml

hyb_protocol: 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts.

scan_protocol: The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA.

label_protocol: Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/mcl

extract_protocol: cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity.


title: Halobacterium Oxygen1 H 00 min dye swap 1

description: reference vs. high oxygen at shift from anaerobic to aerobic

treatment_protocol: 10mL of cells were harvested from turbidostat, pelleted at 13,000rpm for 0.5 min, and snap-frozen in a dry-ice ethanol bath.  Samples were stored at -80C until RNA extraction.


title: HMEC  ox-PAPC 10 mcg/ml  1432059024_G

description: Replicate of HMEC ox-PAPC 10 mcg/ml

tag: Confluent HMEC in 6-well plates were treated in triplicate by ox-PAPC 10 mcg/ml for 4 hours. Cells were harvested and cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity. Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/mcl, and then 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts. The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA. The microarray data was normalized and analyzed by Illumina Inc. BeadStudio software, version 1.5.0.34 (Illumina, Inc. San Diego, CA)


title: HMEC DEP-5 mcg/ml 1432059024_E

description: Replicate of HMEC DEP-5 mcg/ml

tag: Confluent HMEC in 6-well plates were treated in triplicate by DEP-5 mcg/ml for 4 hours. Cells were harvested and cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity. Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/mcl, and then 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts. The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA. The microarray data was normalized and analyzed by Illumina Inc. BeadStudio software, version 1.5.0.34 (Illumina, Inc. San Diego, CA)


title: HMEC  DEP-25  mcg/ml 1432059030_A

description: Replicate of HMEC DEP-25  mcg/ml

tag: Confluent HMEC in 6-well plates were treated in triplicate by DEP-25  mcg/ml for 4 hours. Cells were harvested and cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity. Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/mcl, and then 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts. The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA. The microarray data was normalized and analyzed by Illumina Inc. BeadStudio software, version 1.5.0.34 (Illumina, Inc. San Diego, CA)


title: HMEC  DEP-5 mcg/ml 1432059024_D

description: Replicate of HMEC DEP-5 mcg/ml


title: HMEC  ox-PAPC 20 mcg/ml  1432059026_C

description: Replicate of HMEC ox-PAPC 20 mcg/ml

tag: Confluent HMEC in 6-well plates were treated in triplicate by ox-PAPC 20 mcg/ml for 4 hours. Cells were harvested and cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity. Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/mcl, and then 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts. The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA. The microarray data was normalized and analyzed by Illumina Inc. BeadStudio software, version 1.5.0.34 (Illumina, Inc. San Diego, CA)


title: HMEC  ox-PAPC 20 mcg/ml 1432059026_D

description: Replicate of HMEC ox-PAPC 20 mcg/ml


title: HMEC  ox-PAPC 10 mcg/ml  1432059024_F

description: Replicate of HMEC ox-PAPC 10 mcg/ml


title: HMEC  ox-PAPC 10 mcg/ml  1432059026_B

description: Replicate of HMEC ox-PAPC 10 mcg/ml


title: HMEC  DEP-25  mcg/ml 1432059030_C

description: Replicate of HMEC DEP-25  mcg/ml


title: Halobacterium Oxygen1 L2H -1min 1

description: low oxygen -1min pre-shift vs. reference

source_name: Halobacterium NRC1, anaerobic 1 minute pre-shift

growth_protocol: Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr.  Sample was harvested at 1 minute prior to rapidly shifting to high (~90-100%, 5uM) oxygen for 6 hours, then to low oxygen for 6 hr, and back to high oxygen for 30 min.


title: HMEC  ox-PAPC 40 mcg/ml  1432059026_G

description: Replicate of HMEC ox-PAPC 40 mcg/ml


title: HMEC  DEP 5 mcg/ml + ox-PAPC 40 mcg/ml 1432059028_F

description: Replicate of HMEC DEP 5 mcg/ml  + ox-PAPC 40 mcg/ml

tag: Confluent HMEC in 6-well plates were treated in triplicate by DEP 5 mcg/ml  + ox-PAPC 40 mcg/ml  for 4 hours. Cells were harvested and cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity. Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/mcl, and then 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts. The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA. The microarray data was normalized and analyzed by Illumina Inc. BeadStudio software, version 1.5.0.34 (Illumina, Inc. San Diego, CA)


title: HMEC  DEP 5 mcg/ml + ox-PAPC 40 mcg/ml 1432059028_E


title: Female wildtype/Male wildtype #2 from pooled ICR mice for sex-specificity study

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: The genetic expression profile for pools of 2 males and 2 females is given as a normalized ratio (females over males) as reported from Rosetta Resolver. The reported ratio is the average of two dye-swapped fluorescent reverse pairings. The purpose of this comparison is to highlight sex-specific differences in mouse liver gene expression.

hyb_protocol: Final volume of 3 ml in a flexible plastic enclosure at 40°C on a rotating platform in a hybridization oven. After hybridization for 16−24 h, slides were washed (rocking approx 30s in 6x SSPE, 0.005% sarcosine, then rocking approx 30s in 0.06x SSPE). Protocol taken from PMID: 11283592

scan_protocol: confocal laser scanner (General Scanning, Wilmington, MA; Genetic Microsystems, Woburn, MA; or Axon, Foster City, CA) Protocol taken from PMID: 11283592

data_processing: Rosetta Resolver pipeline

organism: Mus musculus

source_name: frozen adult male mouse liver tissue prepared using Trizol

label_protocol: amino-allyl reverse transcription

extract_protocol: Trizol extraction

tag: Strain

value: ICR

tag: Gender

value: male

tag: Tissue

value: liver

tag: Age

value: 8-9 weeks

source_name: frozen adult female mouse liver tissue prepared using Trizol

value: female


title: Male knockout/Female knockout #3 from STAT5a KO study

description: The genetic expression profile for a single female STAT5a knockout and single male STAT5a knockout is given as a normalized ratio (male ko over female ko) as reported from Rosetta Resolver. The reported ratio is the average of two dye-swapped fluorescent reverse pairings. The purpose of this comparison is to highlight sex-specific differences in mouse liver gene expression.

value: 129JxBlack Swiss


title: HMEC  DEP 5 mcg/ml + oxPAPC 40 mcg/ml 1432059028_G


title: HMEC  DEP-5 mcg/ml 1432059024_H

description: Replicate of HMEC DEP-5 mcg/ml


title: Female wildtype/Male wildtype #2 from ICR mice for sex-specificity study

description: The genetic expression profile for a single male and single female is given as a normalized ratio (female over male) as reported from Rosetta Resolver. The reported ratio is the average of two dye-swapped fluorescent reverse pairings. The purpose of this comparison is to highlight sex-specific differences in mouse liver gene expression.


title: HMEC  ox-PAPC 20 mcg/ml  1432059026_E

description: Replicate of HMEC ox-PAPC 20 mcg/ml


title: HMEC  DEP-25  mcg/ml 1432059030_B

description: Replicate of HMEC DEP-25  mcg/ml


title: HMEC  DEP 5 mcg/ml + ox-PAPC 20 mcg/ml  1432059028_C

description: Replicate of HMEC DEP 5 mcg/ml  + ox-PAPC 20 mcg/ml

tag: Confluent HMEC in 6-well plates were treated in triplicate by DEP 5 mcg/ml  + ox-PAPC 20 mcg/ml  for 4 hours. Cells were harvested and cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity. Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/mcl, and then 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts. The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA. The microarray data was normalized and analyzed by Illumina Inc. BeadStudio software, version 1.5.0.34 (Illumina, Inc. San Diego, CA)


title: Female wildtype/Male wildtype #1 from ICR mice for sex-specificity study


title: HMEC  DEP 5 mcg/ml + ox-PAPC 10  mcg/ml 1432059030_E

description: Replicate of HMEC DEP 5 mcg/ml  + ox-PAPC 10 mcg/ml

tag: Confluent HMEC in 6-well plates were treated in triplicate by DEP 5 mcg/ml  + ox-PAPC 10 mcg/ml  for 4 hours. Cells were harvested and cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity. Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/mcl, and then 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts. The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA. The microarray data was normalized and analyzed by Illumina Inc. BeadStudio software, version 1.5.0.34 (Illumina, Inc. San Diego, CA)


title: HMEC  control 1432059029_H

description: Replicate of HMEC were cultured in DMEM

tag: Confluent HMEC in 6-well plates were cultured in DMEM for 4 hours. Cells were harvested and cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity. Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/mcl, and then 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts. The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA. The microarray data was normalized and analyzed by Illumina Inc. BeadStudio software, version 1.5.0.34 (Illumina, Inc. San Diego, CA)


title: Male knockout/Female knockout #2 from STAT5a KO study


title: HMEC  DEP 5 mcg/ml + ox-PAPC 10  mcg/ml 1432059030_F


title: HMEC  DEP 5 mcg/ml  + ox-PAPC 20 mcg/ml  1432059028_B


title: HMEC  DEP 5 mcg/ml  + ox-PAPC 20 mcg/ml  1432059028_D


title: Female wildtype/Female knockout #3 from STAT5a KO study

description: The genetic expression profile for a single female STAT5a knockout and single female wildtype is given as a normalized ratio (female wt over female ko) as reported from Rosetta Resolver. The reported ratio is the average of two dye-swapped fluorescent reverse pairings. The purpose of this comparison is to highlight genotype-specific differences in mouse liver gene expression.


title: HMEC  DEP 5 mcg/ml  + ox-PAPC 10 mcg/ml 1432059030_D


title: Male knockout/Female knockout #1 from STAT5a KO study


title: Male knockout/Male wildtype #3 from STAT5a KO study

description: The genetic expression profile for a single male and single female is given as a normalized ratio (male ko over male wt) as reported from Rosetta Resolver. The reported ratio is the average of two dye-swapped fluorescent reverse pairings. The purpose of this comparison is to highlight genotype-specific differences in mouse liver gene expression.


title: Male knockout/Male wildtype #1 from STAT5a KO study


title: Male knockout/Male wildtype #2 from STAT5a KO study


title: HMEC control 1432059029_G

description: Replicate of HMEC were cultured in DMEM


title: Female wildtype/Female knockout #1 from STAT5a KO study


title: Female wildtype/Female knockout #2 from STAT5a KO study


title: HMEC control 1432059024_C

description: Replicate of HMEC were cultured in DMEM

tag: Confluent HMEC in 6-well plates were cultured in DMEM for 4 hours. Cells were harvested and cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity. Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/µl, and then 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts. The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA. The microarray data was normalized and analyzed by Illumina Inc. BeadStudio software, version 1.5.0.34 (Illumina, Inc. San Diego, CA)


title: Female wildtype/Male wildtype #3 from STAT5a KO study


title: Female wildtype/Male wildtype #2 from STAT5a KO study

value: 129JxBlack Swiss; Gender:male; Tissue:liver; Age:8-9 weeks

value: 129JxBlack Swiss; Gender:female; Tissue:liver; Age:8-9 weeks


title: Male wildtype/Female wildtype #3 from STAT5b KO study

description: The genetic expression profile for a pool of 3 males and a pool of 3 females is given as a normalized ratio as reported from Rosetta Resolver.  The reported ratio is the average of two dye-swapped fluorescent reverse pairings.  The purpose of this comparison is to highlight the sex-specific differences in mouse liver gene expression.

value: Male

value: Liver

value: Female


title: Female wildtype/Male wildtype #1 from pooled ICR mice for sex-specificity study

description: The genetic expression profile for pools of 3 males and 3 females is given as a normalized ratio (females over males) as reported from Rosetta Resolver. The reported ratio is the average of two dye-swapped fluorescent reverse pairings. The purpose of this comparison is to highlight sex-specific differences in mouse liver gene expression.


title: Female wildtype/Male wildtype #1 from STAT5a KO study

hyb_protocol: Final volume of 3 ml in a flexible plastic enclosure at 40°C on a rotating platform in a hybridization oven. After hybridization for 16−24 h, slides were washed (rocking approx 30s in 6x SSPE, 0.005% sarcosine, then rocking approx 30s in 0.06x SSPE).  Protocol taken from PMID: 11283592


title: Male wildtype/Female wildtype #2 from STAT5b KO study


title: FoxH1 morpholino ZF1221 060629

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

description: Zebrafish embryos

hyb_protocol: The combined Cy3 and Cy5 labeled cDNAs are put in a total volume of 250 ul DEPC H20 and 250 ul of 2X Agilent hybridization buffer. The mixture is then denatured for 2 minutes and applied on the Agillent hybridization chamber/gasket slide in sandwich with the array slide. The hybridization is performed at 65 degre for 16 hours.

scan_protocol: Agilent Scanner

data_processing: IPLab/DeArray

organism: Danio rerio

source_name: control morpholino-injected 40% epiboly-stage zebrafish embryos

label_protocol: 10-15 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Aminoallyl dUTP, after NaOH RNA hydrolysis, the labeled Aminoallyl dUTP cDNA is purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104). The Aminoallyl dUTP cDNAs are then coupled with either Cy3 or Cy5 mono NHS Ester Dyes. The CyDyes labeled cDNAs are then purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104).

extract_protocol: RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns

tag: Zebrafish embryos

source_name: FoxH1 morpholino-injected 40% epiboly-stage zebrafish embryos


title: FoxH1 morpholino ZF1223 Rev 060629

description: Zebrafish embryos


title: FoxH1 morpholino ZF1222 060629

description: Zebrafish embryos


title: ETS1 in HT29 proximal promoter array 1 rep1

status: Public on Jul 27 2007

type: genomic

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E Third St, Jordan Hall 104

institute: Indiana University

description: Chromatin IP signal

hyb_protocol: Hybridization of 2 micrograms of each labeled DNA for 40 hrs at 65 degrees using Agilent ACGH/ChIP-chip hybridization and wash kit.

scan_protocol: Hybridized microarrays were scanned using an Agilent G2565BA microarray scanner.

data_processing: Raw image files were processed with Agilent Feature Extraction software (v. 8.5).

molecule: genomic DNA

source_name: HT29 cells immunoprecipitated

label_protocol: Labeled using random primed klenow based extension

extract_protocol: Phenol Chloroform extraction

tag: anti ETS1 antibody; chromatin immunoprecipitation

source_name: HT29 cells Input DNA (total)

tag: HT29 cells Input DNA


title: Male wildtype/Female wildtype #1 from STAT5b KO study


title: E2F4 in Jurkat proximal promoter array 1 rep2

description: Chromatin IP signal

source_name: Jurkat cells immunoprecipitated

tag: anti E2F4 antibody; chromatin immunoprecipitation

source_name: Jurkat cells Input DNA (total)

tag: Jurkat cells Input DNA


title: E2F4 in Jurkat proximal promoter array 1 rep1

description: Chromatin IP signal


title: E2F4 in Jurkat extended promoter array 1 rep1

description: Chromatin IP signal


title: ETS1 in Jurkat proximal promoter array 1 rep2

description: Chromatin IP signal

hyb_protocol: Hybridization of 2 micrograms of each labeled DNA for 40 hrs at 65 degrees using Agilent ACGH/ChIP-chip hybridization and wash kit

data_processing: Raw image files were processed with Agilent Feature Extraction software (v. 8.5)


title: ETS1 in HT29 proximal promoter array 2 rep1

description: Chromatin IP signal


title: ELF1 in Jurkat proximal promoter array 1 rep2

description: Chromatin IP signal

tag: anti ELF1 antibody; chromatin immunoprecipitation


title: E2F4 in Jurkat proximal promoter array 2 rep2

description: Chromatin IP signal


title: ETS1 in Jurkat proximal promoter array 1 rep3

description: Chromatin IP signal


title: E2F4 in Jurkat proximal promoter array 2 rep1

description: Chromatin IP signal


title: ETS1 in Jurkat extended promoter array 2 rep1

description: Chromatin IP signal


title: ELF1 in Jurkat proximal promoter array 2 rep2

description: Chromatin IP signal


title: ETS1 in Jurkat proximal promoter array 1 rep1

description: Chromatin IP signal

extract_protocol: Chromatin immunoprecipitation

tag: anti ETS1 antibody


title: ETS1 in Jurkat extended promoter array 1 rep1

description: Chromatin IP signal


title: ELF1 in Jurkat proximal promoter array 1 rep1

description: Chromatin IP signal

source_name: Jurkat cells Input DNA (total

tag: anti ELF1 antibody


title: E2F4 in Jurkat extended promoter array 2 rep1

description: Chromatin IP signal


title: RUNX1 in Jurkat extended promoter array 1 rep2

description: Chromatin IP signal

tag: anti RUNX1 antibody; chromatin immunoprecipitation


title: ETS1 in Jurkat proximal promoter array 2 rep3

description: Chromatin IP signal


title: GABPa in Jurkat extended promoter array 2 rep2

description: Chromatin IP signal

tag: anti GABPa antibody; chromatin immunoprecipitation


title: ELF1 in Jurkat proximal promoter array 2 rep1

description: Chromatin IP signal


title: GABPa in Jurkat extended promoter array 1 rep2

description: Chromatin IP signal


title: ETS1 in Jurkat proximal promoter array 2 rep2

description: Chromatin IP signal


title: E2F4 in Jurkat extended promoter array 2 rep2

description: Chromatin IP signal


title: Bj_Bacteroid_Rep5

status: Public on Jul 26 2007

city: Arlington

first: Woo-Suk

last: Chang

state: TX

address: 501 S. Nedderman Dr. , Life Science Building 216

department: Biology

institute: University of Texas at Arlington

description: Transcriptional profiling of bacteroids compared to free-living cells.

hyb_protocol: Both cy3 and cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42 C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42 C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices Corp., Sunnyvale, CA). Signal intensities were analyzed using GenePix Pro 6.0 software (Molecular Devices Corp., Sunnyvale, CA).

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://www.jax.org/staff/churchill/labsite/). Expression values from two technical replicates in each array were combined, averaged, and subsequently subjected to significance analysis of microarray (SAM) data using the SAM package (Tusher et al. 2001). Significant genes were selected based on a 1.5- or 2-fold cut off threshold with a false discovery rate lower than 5%.

organism: Bradyrhizobium diazoefficiens USDA 110

source_name: Bacteroid, replication 3

label_protocol: 20 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined using a Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). Four micrograms of cDNA were used for labeling with either cy3 or cy5 (Armersham) and unincorporated dyes were removed using a Qiaquick PCR purification Kit (Qiagen).

extract_protocol: Standard hot-phenol method

tag: Four-week-old bacteroids were harvested from soybean root nodules.

source_name: Free-living cells, replication 3

tag: Free-living cells. B. japonicum was grown in rich medium.


title: GABPa in Jurkat extended promoter array 2 rep1

description: Chromatin IP signal


title: ELF1 in Jurkat extended promoter array 1 rep2

description: Chromatin IP signal


title: Bj_Bacteroid_Rep3

source_name: Bacteroid, replication 2

source_name: Free-living cells, replication 2


title: Bj_Bacteroid_Rep4


title: ELF1 in Jurkat extended promoter array 1 rep1

description: Chromatin IP signal


title: ETS1 in Jurkat extended promoter array 2 rep2

description: Chromatin IP signal


title: RUNX1 in Jurkat extended promoter array 2 rep1

description: Chromatin IP signal


title: ETS1 in Jurkat proximal promoter array 2 rep1

description: Chromatin IP signal


title: ELF1 in Jurkat extended promoter array 2 rep2

description: Chromatin IP signal


title: E2F4 in Jurkat extended promoter array 1 rep2

description: Chromatin IP signal


title: GABPa in Jurkat extended promoter array 1 rep1

description: Chromatin IP signal


title: Bj_Bacteroid_Rep2

source_name: Free-living cells, replication 1

source_name: Bacteroid, replication 1


title: ELF1 in Jurkat extended promoter array 2 rep1

description: Chromatin IP signal


title: Bj_Salt_Rep2

description: Transcriptional profiling of B. japonicum exposed to the osmotic stress was examined.

source_name: Salt treatment, replication 1

tag: 50 mM NaCl was added in the culture medium.

source_name: Control, replication 2

tag: No NaCl was added in the culture medium.


title: Bj_Salt_Rep3

source_name: Salt treatment, replication 3


title: RUNX1 in Jurkat extended promoter array 1 rep1

description: Chromatin IP signal


title: ETS1 in Jurkat extended promoter array 1 rep2

description: Chromatin IP signal


title: RUNX1 in Jurkat extended promoter array 2 rep2

description: Chromatin IP signal


title: Bj_Bacteroid_Rep1


title: Bj_Minimal_Rich_Rep5

description: Transcriptional profiling of B. japonicum was compared between cells grown in minimal and rich meidum.

source_name: Minimal medium, replication 3

tag: B. japonicum was grown in minimal medium supplemented with glycerol as a carbon source.

source_name: Rich medium, replication 3

tag: B. japonicum was grown in rich medium.


title: Bj_Salt_Rep1

source_name: Control, replication 1

source_name: Salt treatment, replication 2


title: Bj_Minimal_Rich_Rep1

source_name: Minimal medium, replication 1

extract_protocol: Standard hot-phenol method.

source_name: Rich medium, replication 1


title: Bj_Minimal_Rich_Rep6


title: Bj_Minimal_Rich_Rep3

source_name: Minimal medium, replication 2

source_name: Rich medium, replication 2


title: Bj_Minimal_Rich_Rep4


title: Retina/RPE_goggled_3dayE5

city: Philadelphia

first: Alice

middle: M

last: McGlinn

state: PA

address: 602D Richards Building 3700 Hamilton Walk

department: Ophthalmology

institute: University of Pennsylvania School of Medicine

description: Microarray targets were prepared using total RNA from each eye of six chicks from each of the two experimental groups. All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Inc., Santa Clara, CA). Briefly, 3μg of total RNA from each eye was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP. The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 hrs at 45ºC to one of twenty-four Affymetrix GeneChip Chicken Genome Arras. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin.  Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. Using a GeneChip 3000 7G scanner, the fluorescence signal (570nm excitation) was recorded at 2.5μm resolution. Data were collected using GCOS software, (v1.4, Affymetrix), and probe level intensities were exported as .cel files for subsequent summarization and analysis.

hyb_protocol: see manufacturer's website

scan_protocol: see manufacturer's website Scanner:  GeneChip 3000 7G

data_processing: Affymetrix .cel (probe intensity) files were exported from GCOS, and processed using Stratagene’s ArrayAssist Lite v3.1 (Stratagene, La Jolla, CA ) to yield .chp files containing Robust Multichip Analysis (RMA) expression values and Affymetrix flags (Present, Absent, Marginal) for each array.  The normalized microarray signal intensities were then analyzed by the Significance Analysis of Microarrays approach.(SAM).  For the retinas of chicks with 6 hours of unilateral form-deprivation, the SAM analysis indicated few differentially expressed genes; and a 50% false discovery rate was arbitrarily set to yield a list of 112 candidate genes. For the retinas of chicks with 3 days of unilateral form-deprivation, the SAM false discovery rate was set arbitrarily at 14% to yield 296 (i.e., approximately 300) candidate genes.

label: Biotin

organism: Gallus gallus

source_name: Gallus gallus retina/RPE

label_protocol: see manufacturer's website

extract_protocol: Each frozen retina/RPE sample was ground under liquid nitrogen, using a mortar and pestle.  RNA was then isolated from each preparation using Trizol (Invitrogen, Carlsbad, CA) followed by purification and DNase treatment on RNeasy columns (Qiagen,Inc, Valencia, CA). The samples were measured on a NanoDrop ND-1000 UV-Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE) for quantification and purity, with 260/280nm absorbance ratios between 1.8 and 2.1. To evaluate RNA integrity further, an aliquot of each RNA sample was loaded onto an RNA 6000 NanoLab Chip and placed in an Agilent 2100 Bioanalyzer (Agilent Technologies, SantaClara, CA); suitable RNA integrity was established from the electropherograms and gel-images generated by the Bioanalyzer software (data not shown). Aliquots of the RNA samples were stored individually at –80º C.

treatment_protocol: One-day old white Leghorn chicks were housed in brooders with a 12 hr light:dark cycle, using General Electric chroma 50 fluorescent lighting with irradiance of approximately 50μW/cm2 at chick eye level. They received Purina Chick Chow food and water ad libitum. At one week of age and at the onset of the light phase, the chicks were anesthetized with inhalation ether, and a unilateral translucent white plastic goggle was glued to the periorbital feathers to induce ipsilateral form-deprivation myopia, alternating between the left or right eye. After either 6 hrs (n=8) or 3 days (n=8) of goggle wear, the chicks were killed by decapitation. The enucleated eyes were opened at the equator, and the retina/RPE was dissected together from both the goggled and control eyes. The tissues were individually frozen and stored in liquid nitrogen until processed.

tag: White Leghorn

tag: Gender not determined

tag: 10 days old

tag: Young chicks are extremely difficult to sex from external signs.  Post-mortem dissections were not performed.  The chicks were purchased unsexed.


title: Retina/RPE_goggled_3dayC6


title: Retina/RPE_goggled_3dayE4


title: Retina/RPE_goggled_3dayE3


title: Bj_Salt_Rep4

source_name: Control, replication 3


title: Retina/RPE_goggled_3dayE1

source_name: Gallus gallus  retina/RPE


title: Retina/RPE_goggled_3dayC4


title: Retina/RPE_goggled_6hrE4

source_name: Gallus gallus retina RPE

tag: 7 days old


title: Retina/RPE_goggled_3dayC2


title: Retina/RPE_goggled_6hrE5


title: Retina/RPE_goggled_6hrE3


title: Retina/RPE_goggled_6hrE1


title: Retina/RPE_goggled_6hrE2


title: Retina/RPE_goggled_3dayE2


title: E. coli metJ GSNO Sample2 TechRep2

first: Laura

middle: R

last: Jarboe

address: 420 Westwood Pl

department: Chemical and Biomolecular Engineering

institute: University of California, Los Angeles

description: Cells were grown in MOPS media/0.5% glucose and aerobic conditions.

hyb_protocol: Samples were hybridized as specified in the Corning UltraGAPS manual. Slides were blocked and washed as specified in the Corning UltraGAPS manual.

scan_protocol: Slides were scanned immediately after washing with a Virtek/BioRad scanner.

data_processing: Quantification of the scans were performed with ImaGene (Version 6.0.1; BioDiscovery; El Segundo, CA; www.biodiscovery.com); with the results presented in the associated text files. The normalized data VALUE was generated using LOWESS normalization with rank invariant selection, as implemented in lcDNA (receptor.seas.ucla.edu/lcDNA; Hyduke DR, Rohlin L, Kao KC, Liao JC. 2003 A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7(3):227-234.)

organism: Escherichia coli

source_name: E. coli metJ- mid-log aerobic 37C in MOPS glucose

label_protocol: Samples were directly labeled by direct incorporation of labeled dCTP.

extract_protocol: RNA extracted by hot phenol chloroform followed by Qiagen RNA Midi column.

source_name: E. coli metJ- 5 minutes after the addition of 500uM GSNO

treatment_protocol: Treated with 500 micromolar GSNO for 5 minutes prior to harvesting


title: E. coli metJ GSNO Sample2 TechRep1


title: Retina/RPE_goggled_6hrE6


title: Retina/RPE_goggled_3dayC1

tag: Young chicks are extremely difficult to sex from external signs.  Post-mortem dissections were not performed.  The chicks were purchased unsexed


title: Retina/RPE_goggled_3dayE6


title: Retina/RPE_goggled_3dayC5


title: Retina/RPE_goggled_3dayC3


title: Bj_Minimal_Rich_Rep2


title: E. coli metJ GSNO Sample1 TechRep3


title: E. coli metJ GSNO Sample1 TechRep4


title: E. coli metJ GSNO Sample1 TechRep2


title: E. coli wt met GSNO Sample1 TechRep1

source_name: E. coli mid-log aerobic 37C in methionine-supplemented MOPS glucose

source_name: met-supplemented E. coli 5 minutes after the addition of 500uM GSNO


title: Bj_Bacteroid_Rep6

source_name: Free-living cells, replication 3

source_name: Bacteroid, replication 3


title: E. coli wt met GSNO Sample1 TechRep2


title: E. coli metJ GSNO Sample1 TechRep1


title: Retina/RPE_goggled_6hrC5

tag: not determined

tag: 7 days and 10 days


title: E. coli wt 500 GSNO Sample2 TechRep2

source_name: E. coli wt mid-log aerobic 37C in MOPS glucose

source_name: E. coli wt 5 minutes after the addition of 500uM GSNO


title: E. coli dpp 100 GSNO Sample2 TechRep1

source_name: E. coli dpp- mid-log aerobic 37C in MOPS glucose

source_name: E. coli dpp- 5 minutes after the addition of 100uM GSNO

treatment_protocol: Treated with 100 micromolar GSNO for 5 minutes prior to harvesting


title: Retina/RPE_goggled_6hrC6


title: E. coli dpp 100 GSNO Sample2 TechRep2


title: Retina/RPE_goggled_6hrC4


title: E. coli wt 500 GSNO Sample1 TechRep2


title: Retina/RPE_goggled_6hrC2


title: E. coli wt 500 GSNO Sample1 TechRep1


title: E. coli dpp 100 GSNO Sample1 TechRep1


title: E. coli wt 500 GSNO Sample2 TechRep1


title: E. coli wt 100 GSNO Sample2 TechRep1

source_name: E. coli wt 5 minutes after the addition of 100uM GSNO


title: Retina/RPE_goggled_6hr-C1


title: E. coli dpp 100 GSNO Sample1 TechRep2


title: E. coli wt 100 GSNO Sample1 TechRep2


title: E. coli wt 100 GSNO Sample3 TechRep2


title: E. coli wt 100 GSNO Sample3 TechRep1


title: E. coli wt 100 GSNO Sample1 TechRep1


title: E. coli flhDC GSNO Sample2 TechRep2

source_name: E. coli flhDC- mid-log aerobic 37C in MOPS glucose

source_name: E. coli flhDC- 5 minutes after the addition of 500uM GSNO


title: Retina/RPE_goggled_6hrC3

source_name: Gallus gallus retina/RPE


title: E. coli wt 100 GSNO Sample2 TechRep2


title: E. coli flhDC GSNO Sample2 TechRep1


title: E. coli wt cys GSNO Sample1 TechRep1

source_name: E. coli mid-log aerobic 37C in cysteine-supplemented MOPS glucose

source_name: cys-supplemented E. coli 5 minutes after the addition of 500uM GSNO


title: E. coli wt met GSNO Sample2 TechRep2


title: E. coli wt met GSNO Sample2 TechRep1


title: E. coli nsrR GSNO Sample2 TechRep1

source_name: E. coli nsrR- mid-log aerobic 37C in MOPS glucose

source_name: E. coli nsrR- 5 minutes after the addition of 500uM GSNO


title: E. coli flhDC GSNO Sample1 TechRep1


title: E. coli nsrR GSNO Sample2 TechRep2


title: E. coli wt cys GSNO Sample1 TechRep2


title: E. coli flhDC GSNO Sample1 TechRep2


title: E. coli nsrR GSNO Sample1 TechRep2


title: E. coli cysB GSNO Sample1 TechRep1

source_name: E. coli cysB- mid-log aerobic 37C in cys-supplemented MOPS glucose

source_name: E. coli cysB- 5 minutes after the addition of 500uM GSNO


title: Abdominal Aortic Aneurysm Male Pool I

city: Detroit

first: Gerard

last: Tromp

state: MI

address: 3309 Scott Hall, 540 East Canfield Ave

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

description:
Abdominal aorta collected during autopsy within 24 hours post
mortem

hyb_protocol: 1.5 micrograms of labeled cRNA was used for hybridization, and microarrays were washed and stained using standard Illumina BeadChip 6 X 2 protocol, Doc. # 11176837 Rev. E

scan_protocol: Scanned on Illumina BeadStation 500GX using standard Illumina protocol

data_processing: Raw signal values from Illumina BeadStudio Version 1.5.0.34

label: biotin, streptavidin-Cy3

source_name: Total RNA from human abdominal aortic aneurysm

label_protocol:
150 ng of total RNA was amplified and labeled using the
Illumina TotalPrep RNA Amplification Kit (Cat #IL1791),
manual version 0606

extract_protocol:
Guanidinium isothiocyanate, cesium chloride
centrifugation (Sambrook et. al. Molecular Cloning:  a
laboratory manual)

tag: Ethnicity = Caucasian

tag: Tissue = Abdominal Aortic Aneurysm

tag: Sex = M

tag: Pool Size = 4

tag: Average Age = 64.25


title: Control Abdominal Aorta Male Pool I

source_name: Total RNA from human abdominal aorta

tag: Tissue = Normal Abdominal Aorta

tag: Average Age = 62


title: Control Abdominal Aorta 2-M

tag: Age (years) = 59

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 7.4


title: Control Abdominal Aorta 2-F

tag: Sex = F

tag: Age (years) = 51

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 7.7


title: E. coli nsrR GSNO Sample1 TechRep1


title: Control Abdominal Aorta 4-M

tag: Age (years) = 72

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 6.1


title: Control Abdominal Aorta 3-M

tag: Age (years) = 52

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 8.5


title: Control Abdominal Aorta 3-F

tag: Age (years) = 89

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 6.2


title: E. coli wt control DPTA Sample2 TechRep2

source_name: E. coli mid-log aerobic 37C in MOPS glucose

label_protocol: Samples were directly labeled by direct incorporation of labeled dCTP

source_name: E. coli 5 minutes after the addition of DPTA

treatment_protocol: Added DPTA


title: Abdominal Aortic Aneurysm4-M

description: Abdominal aortic aneurysm obtained from surgery to correct.

tag: Ethnicity = Caucasian

tag: Tissue = Abdominal Aortic Aneurysm

tag: Age (years) = 63

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 5.9


title: E. coli cysB GSNO Sample1 TechRep2


title: Control Abdominal Aorta Female Pool

hyb_protocol: 1. 300 ul of hybridization cocktail (all 15 ug cRNA) is assembled for each sample as per the protocol detailed in the Affymetrix GeneChip  Expression Analysis Technical Manual, rev. 2, 2004, Section 2.2. 2. 200 ul of each cocktail (10 ug cRNA) is hybridized to an Affymetrix GeneChip« Human Genome U133 Plus 2.0 array  for 16 hours at 45 C, rotating at 60 rpm in the GeneChip Hybridization Oven 640 (Affymetrix, #800138). 3. Samples are washed and stained on the Genechip  Fluidics Station 450 (Affymetrix, #00-0079), wash protocol EukGE-WS2v5. Stringent/non-stringent buffers and stains prepared as described in the Affymetrix GeneChip  Expression Analysis Technical Manual, rev. 2, 2004, Section 2.3 & 2.4.

scan_protocol: 1. Arrays are scanned by the GeneChip Scanner 3000 with Auto Loader (Affymetrix, #00-0090) Expression analysis settings at ôAll Probe Setsö Scale Factor 500, Normalization = 1.0, No Masking.

data_processing: GCRMA as implemented by R using the Bioconductor package

label: biotin, streptavidin phycoerythrin

label_protocol:
1. Synthesis of cDNA is performed using the GeneChip
Expression 3Æ-Amplification One-Cycle cDNA Synthesis Kit
(Affymetrix, #900431). A starting amount of 5 ug total
RNA is used for each sample, synthesis reactions are
assembled in MicroAmp PCR tubes (PE Biosystems,
#N801-0540) employing master mixes of reaction components
to accommodate all samples, and performed in a Peltier
Thermal Cycler (PTC)-200 DNA Engine (MJ Research).
2. Purification of double-stranded cDNA is performed
using the GeneChip Sample Clean-up Module (Affymetrix,
#900371).
3. 100% of the cDNA product is carried forward to
synthesize biotin labeled cRNA using the GeneChip IVT
Labeling Kit (Affymetrix, #900449). A master mix of IVT
reaction components is assembled and appropriate aliquots
added to each cDNA sample in MicroAmp PCR tubes, and
incubated at 37? C for 16 hours in the MJ Research
PTC-200 DNA Engine.
4. cRNA products are purified using the GeneChip Sample
Clean-up Module (Affymetrix, #900371), and OD readings
are performed as described in step 2 to assess purity
(260/280) and determine the concentration and yield of
biotin labeled cRNA.
5.  The final concentration of labeled cRNA is corrected
based on the starting amount of total RNA (5 ug) and the
amount of cDNA product (100%) utilized in the synthesis
reaction, as described in the Affymetrix GeneChip
Expression Analysis Technical Manual, rev. 2, 2004,
Section 2.1.
6. Using the corrected cRNA concentration (ug/ul), 15 ug
of labeled cRNA is fragmented using 5x Fragmentation
Buffer included with GeneChip Sample Clean-up Module
(Affymetrix, #900371) at 94? C for 35 minutes.

tag: Tissue = Normal Abdominal Aorta

tag: Pool Size = 3

tag: Average Age = 71.3


title: Control Abdominal Aorta 1-M

tag: Sex = M

tag: Age (years) = 65

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 8


title: Abdominal Aortic Aneurysm3-M

tag: Age (years) = 67

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 6.9


title: E. coli wt control DPTA Sample2 TechRep1


title: Abdominal Aortic Aneurysm Female Pool

tag: Sex = F


title: Abdominal Aortic Aneurysm2-F

tag: Age (years) = 68

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 7


title: Hemoragic Shock Lymph Duct Ligation Biological replicate 1

status: Public on Jul 25 2007

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

institute: PHRI-UMNDJ

description: Hemoragic shock Lymph Duc Liagted animals underwent liagtion of the lymphatic vessels, and then cannulation of the femoral artery and jugular vein followed by a laparotomyin in which blood was withdrawn and a mean arterial pressure of 30 mmHg was kept for 90 min.

hyb_protocol: Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix).  Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.

scan_protocol: Images were acquired using the Affymetrix GeneArray Scanner 3000.  Data was extracted using Affymetrix GeneChip Operating Software version 1.0.

data_processing: Data was extracted using Affymetrix GeneChip Operating Software version 1.0.  Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene).  Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.

label: Biotin Label

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Rat Lung

label_protocol: cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com).  Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen).  Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY).  Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.

growth_protocol: Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals.  The animals were fed standard chow and water.  All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.

extract_protocol: Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).

treatment_protocol: The rats were anesthetized as described above and a midline celiotomy was performed.  The efferent mesenteric lymphatic vessel was identified adjacent to the superior mesenteric artery by reflecting the intestinal loops to the left. The lymphatic vessels were bluntly dissected free, following which they were ligated and subsequently divided. Then the femoral artery and jugular vein were cannulated, and a 5cm laparotomy was performed to mimic tissue injury.  Blood was withdrawn from the jugular vein into a syringe containing 100 units of heparin in 0.3 ml of 0.9% saline until a mean arterial pressure (MAP) of 30 mmHg was obtained.  This MAP was maintained for 90 minutes by withdrawing or reinfusing blood as needed.  At the end of the shock period, all the shed blood was returned.  Return of the shed blood restored the MAP to pre-shock levels.  The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed.  Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.

tag: Hemoragic  Shock Lymph Duct Ligation


title: Hemoragic Shock Lymph Duct Ligation Biological replicate 2


title: Control Abdominal Aorta 1-F

tag: Age (years) = 74

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 6.6


title: E. coli wt control DPTA Sample1 TechRep2


title: Sham Shock Lymph Duct Ligation Biological replicate 1

description: Sham-shock Lymph Duc Liagted animals underwent ligation of the lymphatic vessels, and then cannulation of the femoral artery and jugular vein followed by a laparotomy,  no blood was withdrawn and the MAP was kept within normal limits.

treatment_protocol: The rats were anesthetized as described above and a midline celiotomy was performed.  The efferent mesenteric lymphatic vessel was identified adjacent to the superior mesenteric artery by reflecting the intestinal loops to the left. The lymphatic vessels were bluntly dissected free, following which they were ligated and subsequently divided.  Then animals underwent cannulation of the femoral artery and jugular vein followed by a laparotomy; however, no blood was withdrawn and the MAP was kept within normal limits.  The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed.  Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.

tag: Sham Shock  Lymph Duct Ligation


title: Sham Shock Lymph Duct Ligation Biological replicate 2


title: Hemoragic Shock Lymph Duct Ligation Biological replicate 3


title: Abdominal Aortic Aneurysm1-F

tag: Ethnicity = Caucasian

tag: Tissue = Abdominal Aortic Aneurysm

tag: Age (years) = 82

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 7.2


title: Abdominal Aortic Aneurysm Male Pool A

tag: Pool Size = 4

tag: Average Age = 64.25


title: Sham Shock Lymph Duct Ligation Biological replicate 3


title: Sham Shock Biological replicate 1

description: Sham-shock animals underwent cannulation of the femoral artery and jugular vein followed by a laparotomy; however, no blood was withdrawn and the MAP was kept within normal limits.

treatment_protocol: Sham-shock animals (T/SS) underwent cannulation of the femoral artery and jugular vein followed by a laparotomy; however, no blood was withdrawn and the MAP was kept within normal limits.  The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed.  Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.

tag: Sham Shock


title: Hemoragic Shock Biological replicate 2

description: Hemoragic shock animals underwent cannulation of the femoral artery and jugular vein followed by a laparotomy in which  blood was withdrawn and a mean arterial pressure of 30 mmHg was kept for 90 min.

treatment_protocol: Male rats were anesthetized with intraperitoneal (IP) pentobarbital (50mg/kg) and under strict asepsis, the femoral artery and jugular vein were cannulated, and a 5cm laparotomy was performed to mimic tissue injury.  Blood was withdrawn from the jugular vein into a syringe containing 100 units of heparin in 0.3 ml of 0.9% saline until a mean arterial pressure (MAP) of 30 mmHg was obtained.  This MAP was maintained for 90 minutes by withdrawing or reinfusing blood as needed.  At the end of the shock period, all the shed blood was returned.  Return of the shed blood restored the MAP to pre-shock levels.  The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed.  Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.

tag: Hemoragic  Shock


title: Hemoragic Shock Biological replicate 3


title: Abdominal Aortic Aneurysm2-M

tag: Sex = M

tag: Age (years) = 63

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 6.5


title: Sham Shock Biological replicate 2


title: Sham Shock Biological replicate 3


title: Hemoragic Shock Biological replicate 1


title: E. coli wt control DPTA Sample1 TechRep1

extract_protocol: RNA extracted by hot phenol choloroform folled by Qiagen RNA Midi column.


title: Abdominal Aortic Aneurysm1-M

tag: Age (years) = 64

tag: Agilent BioAnalyzer 2100 RNA Integrity Number = 7.1


title: Medicago truncatula 3 dpi with Sinorhizobium meliloti strain 1021 exoY mutant vs strain 1021 wild type. rep5

status: Public on Jul 24 2007

city: St Paul

first: Kathryn

middle: A

last: VandenBosch

state: MN

address: Room 250 BioSci 6022 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: comparison of M.truncatula roots at 3 days post-inoculation with Sinorhizobium meliloti strain 1021 exoY mutant with roots at 3 days post-inoculation with Sinorhizobium meliloti strain 1021 wild type . rep5

hyb_protocol: Microarrays for each time point were hybridized to cDNAs from both Al- treated and control roots, with cDNAs from the two different treatments labeled with Cy5 and Cy3 dyes. Each hybridization was repeated at least six times to account for technical variability, with triplicates of each dye combination to control for dye effects. A modified two-step hybridization reaction was performed as described in the 3DNA Array 900 Expression Array Detection Kit (Genisphere).

scan_protocol: Microarray slides were scanned using an GenePix4000B (Axon) two-laser scanner and image analysis was performed using GenePix 5.0 (Axon) software

data_processing: Background-subtracted mean intensities for both tissues were log2 transformed and normalized using lowess and ANOVA

organism: Medicago truncatula

source_name: Medicago truncatula 3 days post-inoculation with Sinorhizobium meliloti strain 1021 wild type. rep5

label_protocol: A 66 mg aliquot of each pooled RNA sample was used for cDNA synthesis with random primers using a 3DNA Array 50 Expression Array Detection Kit (Genisphere). One half of the aliquot was labeled during cDNA synthesis with Cy3 dye while the other half was labeled with Cy5 dye using a 3DNA Array 900 Expression Array Detection Kit for cDNA Microarrays (Genisphere, Inc.,Hatfield, PA). cDNA was synthesized following instructions from 3DNA Array 900 Expression Array Detection Kit Appendix A (Genisphere Inc.).

growth_protocol: Medicago truncatula seeds from each line were germinated as previously described (Penmetsa and Cook, 2000). M. truncatula cv. Jemalong A17 seeds were isolated from crushed pods and scarified in concentrated sulfuric acid for 10-12 minutes {Penmetsa, 2000 #5901}.  Scarified seeds were rinsed > 6 times in sterile distilled water, incubated at 4oC overnight, rinsed > 6 times in sterile distilled water and germinated 1 day on 1% agar plates (Sigma, A7921), turned vertically and placed in the dark.  Germinated seedlings (30-50 per plate) were placed on 25 cm x 25 cm Buffered Nod Media (BNM) pH 6.5, 1.5% agar plates. {Engstrom, 2002 #2626}.  BNM plates were supplemented with 1mM of the ethylene synthesis inhibitor a-aminoisobutyric acid (AIB) to facilitate nodulation {Satoh, 1980 #5903; Peters, 1989 #5909; Engstrom, 2002 #2626}.  Seedlings were grown at 25oC under fluorescent lights in a 16:8 hour light:dark cycle for 5 days with roots covered by foil.  One day before inoculation, any roots that had grown down into the agar were placed back on top of the agar.  Roots were inoculated 5 days after transfer to BNM plates.  Saturated bacterial cultures were washed 2-3 times in 1/2x BNM pH 6.5, and resuspended at OD600 = 0.05.  Twenty-five mLs of the appropriate inoculum was applied to each 25 x 25 cm plate.  After harvesting of roots, at least 5 plants were left on each plate and observed for 1 month to verify nodulation phenotype and lack of contamination. Roots were harvested 3 days after inoculation with bacterial suspensions.  Roots from >50 plants per experiment were dipped in liquid nitrogen and then cut away from the shoot and from the bottom 0.5 cm of the root tip.  Roots were frozen at -80oC until RNA was prepared

extract_protocol: RNA was isolated using the RNAeasy Plant Mini Kit (Qiagen 74904).  RNA was DNased with RNase-free DNase (Qiagen 79254).  DNased RNA was pooled from 5 separate experiments for each S. meliloti inoculum strain treatment.

tag: Medicago truncatula; lines - A17; tissue- roots; age - 8 days; treatment - 3 days after Sinorhizobium meliloti strain 1021 wild type inoculation

source_name: Medicago truncatula 3 days post-inoculation with Sinorhizobium meliloti strain 1021 exoY mutant. rep5

tag: Medicago truncatula; lines - A17; tissue- roots; age - 8 days; treatment - 3 days after Sinorhizobium meliloti strain 1021 exoY  inoculation


title: Medicago truncatula 3 dpi with Sinorhizobium meliloti strain 1021 exoY mutant vs strain 1021 wild type. rep3

description: comparison of M.truncatula roots at 3 days post-inoculation with Sinorhizobium meliloti strain 1021 exoY mutant with roots at 3 days post-inoculation with Sinorhizobium meliloti strain 1021 wild type. rep3

source_name: Medicago truncatula 3 days post-inoculation with Sinorhizobium meliloti strain 1021 exoY mutant. rep3

source_name: Medicago truncatula 3 days post-inoculation with Sinorhizobium meliloti strain 1021 wild type. rep3


title: Control Abdominal Aorta Male Pool A

tag: Tissue = Normal Abdominal Aorta

tag: Average Age = 62


title: Medicago truncatula 3 dpi with Sinorhizobium meliloti strain 1021 exoY mutant vs strain 1021 wild type. rep6

description: comparison of M.truncatula roots at 3 days post-inoculation with Sinorhizobium meliloti strain 1021 exoY mutant with roots at 3 days post-inoculation with Sinorhizobium meliloti strain 1021 wild type . rep6

source_name: Medicago truncatula 3 days post-inoculation with Sinorhizobium meliloti strain 1021 wild type. rep6

source_name: Medicago truncatula 3 days post-inoculation with Sinorhizobium meliloti strain 1021 exoY mutant. rep6


title: J1501 KCl 0min vs sigB KCl 0min (2)

status: Public on Jul 20 2007

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47669.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1900, 15130; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.62; Parameter Scan Time = 09:16:29; Parameter PMT Volts = 720; Parameter Scan Date = 2003-12-17; Parameter Pixel Size = 10; Parameter Laser on time = 71725; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.11; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.62; Parameter Scan Time = 09:16:29; Parameter PMT Volts = 760; Parameter Scan Date = 2003-12-17; Parameter Pixel Size = 10; Parameter Laser on time = 71687; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 4.99; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri

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

organism: Streptomyces coelicolor

source_name: J1501 KCl 0min

label_protocol: not provided

extract_protocol: not provided

tag: J1501 KCl 0min

source_name: sigB KCl 0min

tag: sigB KCl 0min


title: sigB KCl 0min vs 50 min

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47419.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1970, 15240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.84; Parameter Scan Time = 10:17:47; Parameter PMT Volts = 700; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71673; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.32; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.84; Parameter Scan Time = 10:17:47; Parameter PMT Volts = 750; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71635; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 4.98; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri

source_name: sigB KCl 50min

tag: sigB KCl 50min


title: Medicago truncatula 3 dpi with Sinorhizobium meliloti strain 1021 exoY mutant vs strain 1021 wild type. rep4

description: comparison of M.truncatula roots at 3 days post-inoculation with Sinorhizobium meliloti strain 1021 exoY mutant with roots at 3 days post-inoculation with Sinorhizobium meliloti strain 1021 wild type . rep4

source_name: Medicago truncatula 3 days post-inoculation with Sinorhizobium meliloti strain 1021 wild type. rep4

source_name: Medicago truncatula 3 days post-inoculation with Sinorhizobium meliloti strain 1021 exoY mutant. rep4


title: Medicago truncatula 3 dpi with Sinorhizobium meliloti strain 1021 exoY mutant vs strain 1021 wild type. rep2

description: comparison of M.truncatula roots at 3 days post-inoculation with Sinorhizobium meliloti strain 1021 exoY mutant with roots at 3 days post-inoculation with Sinorhizobium meliloti strain 1021 wild type. rep2

source_name: Medicago truncatula 3 days post-inoculation with Sinorhizobium meliloti strain 1021 exoY mutant. rep2

source_name: Medicago truncatula 3 days post-inoculation with Sinorhizobium meliloti strain 1021 wild type. rep2


title: J1501 KCl 0min vs sigB KCl 0min

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47415.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1870, 15430; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.05; Parameter Scan Time = 10:39:50; Parameter PMT Volts = 700; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71695; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.16; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.05; Parameter Scan Time = 10:39:50; Parameter PMT Volts = 780; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71657; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.06; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri


title: sigB KCl 0min vs 05 min

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47416.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1550, 15570; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.02; Parameter Scan Time = 10:35:29; Parameter PMT Volts = 700; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71691; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.36; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.02; Parameter Scan Time = 10:35:29; Parameter PMT Volts = 780; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71653; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.05; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri

source_name: sigB KCl 5min

tag: sigB KCl 5min


title: J1501 KCl 0min vs 30 min (2)

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47670.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 15010; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.74; Parameter Scan Time = 09:21:40; Parameter PMT Volts = 720; Parameter Scan Date = 2003-12-17; Parameter Pixel Size = 10; Parameter Laser on time = 71731; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.74; Parameter Scan Time = 09:21:40; Parameter PMT Volts = 770; Parameter Scan Date = 2003-12-17; Parameter Pixel Size = 10; Parameter Laser on time = 71693; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 4.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri

source_name: J1501 KCl 30min

tag: J1501 KCl 30min


title: sigB KCl 0min vs 80 min

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47420.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2000, 15410; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.75; Parameter Scan Time = 10:11:52; Parameter PMT Volts = 700; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71667; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.75; Parameter Scan Time = 10:11:52; Parameter PMT Volts = 780; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71629; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 4.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri

source_name: sigB KCl 80min

tag: sigB KCl 80min


title: J1501 KCl 0min vs 50min

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46306.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1930, 15270; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.29; Parameter Scan Time = 09:36:43; Parameter PMT Volts = 750; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68411; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.29; Parameter Scan Time = 09:36:43; Parameter PMT Volts = 780; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68373; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 4.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri

source_name: J1501 KCl 50min

tag: J1501 KCl 50min


title: sigB KCl 0min vs 15 min

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47417.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1550, 15010; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.99; Parameter Scan Time = 10:31:04; Parameter PMT Volts = 700; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71686; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.15; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.99; Parameter Scan Time = 10:31:04; Parameter PMT Volts = 780; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71648; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.03; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri

source_name: sigB KCl 15min

tag: sigB KCl 15min


title: sigB KCl 0min vs 30 min

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47418.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1550, 15140; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.93; Parameter Scan Time = 10:25:53; Parameter PMT Volts = 690; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71681; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.93; Parameter Scan Time = 10:25:53; Parameter PMT Volts = 780; Parameter Scan Date = 2003-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 71643; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.02; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri

source_name: sigB KCl 30min

tag: sigB KCl 30min


title: D5 aggregate culture, 9A1, rep 2

status: Public on Jul 19 2007

city: Houston

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Gene expression data from 9A1 BMEL cells cultured under aggregate conditions.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Expression Array 430a . GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (non-upgraded).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 (non-upgraded).

data_processing: The data were analyzed with the Bioconductor affy (Gautier L, Cope L, Bolstad BM, et al. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (Oxford, England). 2004;20(3):307-315) package using R 2.3.1 and RMA (Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (Oxford, England). 2003;4(2):249-264) as the normalization method.

label: biotin

source_name: bipotential mouse embryonic liver cell line 9A1, aggregate culture 5 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

extract_protocol: RNeasy Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.  RNA had an 18S/28S ratio greater than 1.7, a 260/230 ratio greater than 1.5, and a lack of visual RNA degradation on Agilent 2100 Bioanalyzer electropherograms (Agilent Technologies Inc.).

treatment_protocol: aggregate culture (Strick-Marchand H, Weiss MC. Inducible differentiation and morphogenesis of bipotential liver cell lines from wild-type mouse embryos. Hepatology. 2002;36:794-804)

tag: Strain

value: CBA/J x C57Bl/6J

tag: Tissue

value: cell lines derived from dpc14 embryonic mouse liver

tag: Cell line

tag: Culture condition

value: aggregate


title: D5 aggregate culture, 14B3, rep 2

description: Gene expression data from 14B3 BMEL cells cultured under aggregate conditions.

source_name: bipotential mouse embryonic liver cell line 14B3, aggregate culture 5 days


title: Matrigel culture, 14B3, rep 1

description: Gene expression data from 14B3 BMEL cells cultured under Matrigel conditions.

source_name: bipotential mouse embryonic liver cell line 14B3, Matrigel culture 5 days

treatment_protocol: Matrigel culture (Strick-Marchand H, Weiss MC. Inducible differentiation and morphogenesis of bipotential liver cell lines from wild-type mouse embryos. Hepatology. 2002;36:794-804)

value: Matrigel


title: D5 aggregate culture, 14B3, rep 1


title: Matrigel culture, 14B3, rep 2

source_name: bipotential mouse embryonic liver cell line 14B3, Matrigel culture 10 days


title: Matrigel culture, 9A1, rep 1

description: Gene expression data from 9A1 BMEL cells cultured under Matrigel conditions.

source_name: bipotential mouse embryonic liver cell line 9A1, Matrigel culture 10 days


title: Matrigel culture, 9A1, rep 2


title: basal culture, 9A1, rep 2

description: Gene expression data from 9A1 BMEL cells cultured under basal conditions.

source_name: bipotential mouse embryonic liver cell line 9A1, basal culture

treatment_protocol: basal culture (Strick-Marchand H, Weiss MC. Inducible differentiation and morphogenesis of bipotential liver cell lines from wild-type mouse embryos. Hepatology. 2002;36:794-804)

value: basal


title: basal culture, 14B3, rep 2

description: Gene expression data from 14B3 BMEL cells cultured under basal conditions.

source_name: bipotential mouse embryonic liver cell line 14B3, basal culture


title: D5 aggregate culture, 9A1, rep 1


title: J1501 KCl 0min vs 15min

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46304.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1910, 15360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.11; Parameter Scan Time = 09:24:31; Parameter PMT Volts = 720; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68399; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.25; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.11; Parameter Scan Time = 09:24:31; Parameter PMT Volts = 780; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68361; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 4.98; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri

source_name: J1501 KCl 0min

source_name: J1501 KCl 15min

tag: J1501 KCl 15min


title: J1501 KCl 0min vs 80min

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46307.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1770, 15290; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.35; Parameter Scan Time = 09:41:15; Parameter PMT Volts = 730; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68415; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.18; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.35; Parameter Scan Time = 09:41:15; Parameter PMT Volts = 780; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68377; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 4.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri

source_name: J1501 KCl 80min

tag: J1501 KCl 80min


title: J1501 KCl 0min vs 05min

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46303.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1750, 15220; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.98; Parameter Scan Time = 09:14:47; Parameter PMT Volts = 710; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68389; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.30; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.98; Parameter Scan Time = 09:14:47; Parameter PMT Volts = 780; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68351; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 4.93; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri

source_name: J1501 KCl 5min

tag: J1501 KCl 5min


title: Medicago truncatula 3 dpi with Sinorhizobium meliloti strain 1021 exoY mutant vs strain 1021 wild type. rep1

description: comparison of M.truncatula roots at 3 days post-inoculation with Sinorhizobium meliloti strain 1021 exoY mutant with roots at 3 days post-inoculation with Sinorhizobium meliloti strain 1021 wild type. rep1

source_name: Medicago truncatula 3 days post-inoculation with Sinorhizobium meliloti strain 1021 exoY mutant. rep1

tag: Medicago truncatula; lines - A17; tissue- roots; age - 8 days; treatment - 3 days after Sinorhizobium meliloti strain 1021 exoY  inoculation

source_name: Medicago truncatula 3 days post-inoculation with Sinorhizobium meliloti strain 1021 wild type. rep1

tag: Medicago truncatula; lines - A17; tissue- roots; age - 8 days; treatment - 3 days after Sinorhizobium meliloti strain 1021 wild type inoculation


title: basal culture, 14B3, rep 1


title: J1501 KCl 0min vs 30min

description:
Simple annotation: sigma factors, salt treatment, unspecified
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46305.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1930, 15520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.20; Parameter Scan Time = 09:32:12; Parameter PMT Volts = 750; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68407; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 5.22; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.20; Parameter Scan Time = 09:32:12; Parameter PMT Volts = 780; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 68369; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81970]; Parameter Laser Power = 4.99; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nitsara,,Karoonuthaisiri

tag: J1501 KCl 0min

source_name: J1501 KCl 30min


title: basal culture, 9A1, rep 1


title: N2a (red, channel 2) vs. lin-4a (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14583.gif

scan_protocol: not provided

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

organism: Caenorhabditis elegans

source_name: lin-4a (green)

tag: lin-4a (green)

source_name: N2a (red)

tag: N2a (red)


title: N2b (red, channel 2) vs. lin-4b (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14584.gif

source_name: lin-4b (green)

tag: lin-4b (green)

source_name: N2b (red)

tag: N2b (red)


title: N2c (red, channel 2) vs. lin-4c (green, channel 1)

description:
Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14585.gif

source_name: lin-4c (green)

tag: lin-4c (green)

source_name: N2c (red)

tag: N2c (red)


title: Basal epidermal cells (+/+) +UVB (3) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50225.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 8280; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April 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 = 40.21; Parameter Scan Time = 12:36:15; Parameter PMT Volts = 590; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 171712; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April 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 = 40.21; Parameter Scan Time = 12:36:15; Parameter PMT Volts = 690; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 170709; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.25; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Reference (brain, liver, neonate, whole dorsal skin) (20ug)

source_name: Basal epidermal cells (+/+) +UVB (3) (20ug)


title: Basal epidermal cells (KitW-v/KitW-v) +UVB (2) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50233.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 8000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April 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 = 41.03; Parameter Scan Time = 15:15:28; Parameter PMT Volts = 590; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 171870; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April 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 = 41.03; Parameter Scan Time = 15:15:28; Parameter PMT Volts = 740; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 170867; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.28; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

tag: Reference (brain, liver, neonate, whole dorsal skin) (20ug)

source_name: Basal epidermal cells (KitW-v/KitW-v) +UVB (2) (20ug)


title: Basal epidermal cells (+/+) +UVB (2) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50224.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 8040; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April 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 = 40.06; Parameter Scan Time = 12:22:21; Parameter PMT Volts = 590; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 171697; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April 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 = 40.06; Parameter Scan Time = 12:22:21; Parameter PMT Volts = 690; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 170694; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.24; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Basal epidermal cells (+/+) +UVB (2) (20ug)