title: mouse embryonic headfold

description:
Date :	5/4/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	none
Route :	none
Dose :	none
Time :	4-8 somite stage
Intervention :	none
Risk: untreated control embryos
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = embryo
Keywords = headfold
Lot batch = AM613


title: MeHg: PK11195 intervention at 4.5h

status: Public on Mar 11 2004

type: RNA

city: Louisville

first: Thomas

middle: B

last: Knudsen

state: KY

address: 501 S Preston St

department: Birth Defects Center

country: USA

institute: University of Louisville

description:
Date :	4/29/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	4.5 hrs post-injection
Intervention :	4.0 mg/kg PK11195 co-administered
Risk: anticipated remediation to <10% malformations
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = methylmercury
Keywords = PK11195
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = SC906

molecule: total RNA

organism: Mus musculus

source_name: 5.0 mg/kg MeHg + PK11195

source_name: MeHg treated prosencephalon


title: Hypoxia: PK11195 intervention

description:
Date :	5/11/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., 16-18 somite stage
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	oxygenation
Route :	whole embryo culture
Dose :	5% oxygen
Time :	2.0 hrs in culture
Intervention :	5.0 uM PK11195
Risk: remediated to ~25% malformed
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	6-8 forebrains pooled
Hybridization extract preparation :	2 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = embryo
Keywords = hypoxia
Keywords = oxygen
Keywords = PK11195
Keywords = microphthalmia
Lot batch = AM660

source_name: 5% oxygen + PK11195 at 2.0h

source_name: forebrain from 5% oxygen at 2.0h


title: optic vesicle stage in mouse

description:
Date :	6/26/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	optic vesicle
Treatments applied
Agent :	none
Route :	none
Dose :	none
Time :	16-20 somite stage
Intervention :	none
Risk: none
Conditional biomarker: p53 protein induction not observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	optic vesicles pooled from 30-40 embryos of 5 litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = eye development
Keywords = embryo
Keywords = mouse
Lot batch = AN090

source_name: optic vesicle, mouse embryos

source_name: headfold, mouse embryo at 8 d.p.c.


title: Hypoxia: reoxygenation

description:
Date :	6/13/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., 16-18 somite stage
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	oxygenation
Route :	whole embryo culture
Dose :	5% oxygen
Time :	2.0 hrs in culture
Intervention :	21% oxygen + 3.0 hrs
Risk: >60% malformed at 24h
Conditional biomarker: p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	6-8 forebrains pooled
Hybridization extract preparation :	2 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = embryo
Keywords = hypoxia
Keywords = oxygen
Keywords = microphthalmia
Lot batch = AO021

source_name: 5% oxygen + 21% oxygen (3.0h)


title: Hypoxia in embryo culture

description:
Genotype :	wild-type
Stage :	9 d.p.c., 16-18 somite stage
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	oxygenation
Route :	whole embryo culture
Dose :	5% oxygen
Time :	2.0 hrs in culture
Intervention :	none
Risk: >60% malformed at 24h
Conditional biomarker: p53 protein induction
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	6-8 forebrains pooled
Hybridization extract preparation :	2 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = embryo
Keywords = hypoxia
Keywords = oxygen
Keywords = microphthalmia
Lot batch = AM619

source_name: forebrain from 21% oxygen at 2.0h


title: MeHg: Ro5-4864 at 4.5h on 9 d.p.c.

description:
Date	6/12/2003
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	4.5 hrs post-injection
Intervention :	4.0 mg/kg Ro5-4864 co-administered
Risk: estimated 20% risk of encephalopathy
Conditional biomarker: unknown
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots
Keywords = methylmercury
Keywords = Ro5-4864
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = SD163


title: mouse embryonic forebrain

description:
Date :	5/8/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	saline control
Route :	single i.p. injection
Dose :	0.0 mg/kg
Time :	3.0 hrs post-injection
Intervention :	none
Risk: none (control)
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = embryo
Keywords = forebrain
Lot batch = AE333/AE8384

source_name: control prosencephalon 9 d.p.c.


title: MeHg: PK11195 intervention at 4.5h

description:
Date :	3/29/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	4.5 hrs post-injection
Intervention :	4.0 mg/kg PK11195 co-administered
Risk: anticipated remediation to <10% malformations
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = methylmercury
Keywords = PK11195
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = SC860


title: MeHg: PK11195 intervention at 4.5h

description:
Date :	3/29/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	4.5 hrs post-injection
Intervention :	4.0 mg/kg PK11195 co-administered
Risk: anticipated remediation to <10% malformations
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = methylmercury
Keywords = PK11195
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = SC862


title: MeHg: Ro5-4864 at 4.5h on 9 d.p.c.

description:
Date	6/12/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	4.5 hrs post-injection
Intervention :	4.0 mg/kg Ro5-4864 co-administered
Risk: estimated 20% risk of encephalopathy
Conditional biomarker: unknown
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots
Keywords = methylmercury
Keywords = Ro5-4864
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = SC907


title: MeHg: PK11195 intervention at 6.0h

description:
Date :	3/29/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	6.0 hrs post-injection
Intervention :	4.0 mg/kg PK11195 co-administered
Risk: anticipated remediation to <10% malformations
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = methylmercury
Keywords = PK11195
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = SC851


title: MeHg: PK11195 intervention at 6.0h

description:
Date :	3/29/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	6.0 hrs post-injection
Intervention :	4.0 mg/kg PK11195 co-administered
Risk: anticipated remediation to <10% malformations
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = methylmercury
Keywords = PK11195
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = SC850


title: MeHg: PK11195 intervention at 3.0h

description:
Date :	3/21/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	3.0 hrs post-injection
Intervention :	4.0 mg/kg PK11195 co-administered
Risk: anticipated remediation to <10% malformations
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = methylmercury
Keywords = PK11195
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = SC857


title: mouse embryonic forebrain

description:
Date :	6/29/01
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	saline control
Route :	single i.p. injection
Dose :	0.0 mg/kg
Time :	3.0 hrs post-injection
Intervention :	none
Risk: none (control)
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = embryo
Keywords = forebrain
Lot batch = AE334/AO71614


title: MeHg: PK11195 intervention at 3.0h

description:
Date :	3/21/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	3.0 hrs post-injection
Intervention :	4.0 mg/kg PK11195 co-administered
Risk: anticipated remediation to <10% malformations
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = methylmercury
Keywords = PK11195
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = SC856


title: 5.0 mg/kg MeHg forebrain at 24.0h

description:
Date :	10/28/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	24 hrs post-injection
Intervention :	none
Risk: estimated 20% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	dinitrophenol-11-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-DNP with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AF623

source_name: saline - control prosencephalon


title: 5.0 mg/kg MeHg forebrain at 24.0h

description:
Date :	10/29/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	24 hrs post-injection
Intervention :	none
Risk: estimated 20% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	dinitrophenol-11-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-DNP with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AF625


title: 5.0 mg/kg MeHg forebrain at 12.0h

description:
Date :	10/16/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	12 hrs post-injection
Intervention :	none
Risk: estimated 20% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AG364


title: 5.0 mg/kg MeHg forebrain at 6.0h

description:
AE318
Date :	4/13/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	6.0 hrs post-injection
Intervention :	none
Risk: estimated 20% incraesed risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	dinitrophenol-11-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-DNP with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease


title: 5.0 mg/kg MeHg forebrain at 12.0h

description:
Date :	10/3/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	12 hrs post-injection
Intervention :	none
Risk: estimated 20% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	dinitrophenol-11-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-DNP with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AG363

source_name: methylmercury-treated


title: 5.0 mg/kg MeHg forebrain at 4.5h

description:
Date :	1/21/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	4.5 hrs post-injection
Intervention :	none
Risk: estimated 20% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	dinitrophenol-11-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-DNP with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AD605


title: 5.0 mg/kg MeHg forebrain at 4.5h

description:
Date :	10/4/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	4.5 hrs post-injection
Intervention :	none
Risk: estimated 20% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	dinitrophenol-11-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-DNP with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AG673


title: 5.0 mg/kg MeHg forebrain at 12.0h

description:
Date :	8/23/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	12 hrs post-injection
Intervention :	none
Risk: estimated 20% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	dinitrophenol-11-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-DNP with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AF604


title: 5.0 mg/kg MeHg forebrain at 6.0h

description:
Date :	4/5/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	6.0 hrs post-injection
Intervention :	none
Risk: 20% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	dinitrophenol-11-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-DNP with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AE319


title: 5.0 mg/kg MeHg forebrain at 3.0h

description:
Date :	10/9/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	3.0 hrs post-injection
Intervention :	none
Risk: estimated 20% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	dinitrophenol-11-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-DNP with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AG674


title: 5.0 mg/kg MeHg forebrain at 3.0h

description:
Date :	3/10/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	3.0 hrs post-injection
Intervention :	none
Risk: estimated 20% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	dinitrophenol-11-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-DNP with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AE194


title: 10.0 mg/kg MeHg at 3.0h

description:
Date :	5/30/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	10 mg/kg
Time :	3 hrs post-injection
Intervention :	none
Risk: 40% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AO092

source_name: saline - control


title: 5.0 mg/kg MeHg at 3.0h

description:
Date :	5/29/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	3 hrs post-injection
Intervention :	none
Risk: estimated 20% incraesed risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AO018


title: 5.0 mg/kg MeHg forebrain at 1.5h

description:
Date :	8/23/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	1.5 hrs post-injection
Intervention :	none
Risk: estimated 20% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	dinitrophenol-11-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-DNP with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AF620


title: 2.5 mg/kg MeHg at 3.0h

description:
Date :	6/12/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	2.5 mg/kg
Time :	3 hrs post-injection
Intervention :	none
Risk: NOAEL (no increased risk for malformations)
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AO044


title: 5.0 mg/kg MeHg at 3.0h

description:
Date :	5/29/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	3 hrs post-injection
Intervention :	none
Risk: estimated 20% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AO017


title: 10.0 mg/kg MeHg at 3.0h

description:
Date :	5/30/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	10 mg/kg
Time :	3 hrs post-injection
Intervention :	none
Risk: 40% increased risk for encephalopathy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AO091


title: 2.5 mg/kg MeHg at 3.0h

description:
Date :	6/12/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	2.5 mg/kg
Time :	3 hrs post-injection
Intervention :	none
Risk: NOAEL (no increased risk of malformation)
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AO045


title: 1.25 mg/kg MeHg forebrain at 3.0h

description:
Date :	6/11/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	1.25 mg/kg
Time :	3 hrs post-injection
Intervention :	none
Risk: subNOAEL (no increased risk of malformation)
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AO026


title: 5.0 mg/kg MeHg forebrain at 1.5h

description:
Date :	8/23/2000
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	5.0 mg/kg
Time :	1.5 hrs post-injection
Intervention :	none
Risk: estimated 20% increased risk for encephalopahy
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	dinitrophenol-11-dCTP, biotinyl-11-dCTP
Hybridization condition :	56-59oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-DNP with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AF619


title: 1.25 mg/kg MeHg forebrain at 3.0h

description:
Date :	6/11/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9 d.p.c., Theiler stage 14
Tissue :	forebrain & surrounding tissue
Treatments applied
Agent :	methylmercury
Route :	single i.p. injection
Dose :	1.25 mg/kg
Time :	3 hrs post-injection
Intervention :	none
Risk: subNOAEL (no increased risk for malformations)
Conditional biomarker: no p53 protein induction observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	10-12 forebrains pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots

Keywords = methylmercury
Keywords = forebrain
Keywords = embryo
Keywords = Fetal Minamata Disease
Lot batch = AO027


title: EtOH: Ro5-4864 in C57BL/6N mice

description:
Date :	9/17/2002
Original sample
Species :	Mouse
Strain :	C57BL/6N
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	ethanol
Route :	single i.p. injection
Dose :	2.9 g/kg
Time :	3 hrs post-injection
Intervention :	4.0 mg/kg Ro5-4864 co-administered
Risk: unknown
Conditional biomarker: weak p53 protein induction
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = ethanol
Keywords = alcohol-related birth defects
Keywords = FAS
Keywords = genetic susceptibility
Keywords = Ro5-4864
Lot batch = SD284

source_name: 2.9 g/kg EtOH + Ro5-4864 headfold

source_name: 2.9 g/kg EtOH headfold at 3.0h


title: EtOH: PK11195 in C57BL/6J mice

description:
Date :	1/21/2003
Original sample
Species :	Mouse
Strain :	C57BL/6J
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	ethanol
Route :	single i.p. injection
Dose :	2.9 g/kg
Time :	3 hrs post-injection
Intervention :	4.0 mg/kg PK11195 co-administered
Risk: unknown
Conditional biomarker: no p53 protein induction observed
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = ethanol
Keywords = alcohol-related birth defects
Keywords = FAS
Keywords = genetic susceptibility
Keywords = PK11195
Lot batch = SD841

source_name: 2.9 g/kg EtOH + PK11195 headfold


title: EtOH: PK11195 in C57BL/6N mice

description:
Date :	10/3/2002
Original sample
Species :	Mouse
Strain :	C57BL/6N
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	ethanol
Route :	single i.p. injection
Dose :	2.9 g/kg
Time :	3 hrs post-injection
Intervention :	4.0 mg/kg PK11195 co-administered
Risk: no increased risk for malformation anticipated
Conditional biomarker: no p53 protein induction observed
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = ethanol
Keywords = alcohol-related birth defects
Keywords = FAS
Keywords = genetic susceptibility
Keywords = PK11195
Lot batch = SD333


title: EtOH: Ro5-4864 in C57BL/6N mice

description:
Date :	9/17/2002
Original sample
Species :	Mouse
Strain :	C57BL/6N
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	ethanol
Route :	single i.p. injection
Dose :	2.9 g/kg
Time :	3 hrs post-injection
Intervention :	4.0 mg/kg Ro5-4864 co-administered
Risk: unknown
Conditional biomarker: weak p53 protein induction
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = ethanol
Keywords = alcohol-related birth defects
Keywords = FAS
Keywords = genetic susceptibility
Keywords = Ro5-4864
Lot batch = SD283


title: EtOH: PK11195 in C57BL/6J mice

description:
Date :	11/6/2002
Original sample
Species :	Mouse
Strain :	C57BL/6J
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	ethanol
Route :	single i.p. injection
Dose :	2.9 g/kg
Time :	3 hrs post-injection
Intervention :	4.0 mg/kg PK11195 co-administered
Risk: unknown
Conditional biomarker: no p53 protein induction observed
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = ethanol
Keywords = alcohol-related birth defects
Keywords = FAS
Keywords = genetic susceptibility
Keywords = PK11195
Lot batch = SD842


title: EtOH: C57BL/6N headfold at 3.0h

description:
Date :	9/5/2002
Original sample
Species :	Mouse
Strain :	C57BL/6N
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	ethanol
Route :	single i.p. injection
Dose :	2.9 g/kg
Time :	3 hrs post-injection
Intervention :	none
Risk: no increased risk for malformations
Conditional biomarker: weak p53 protein induction
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = ethanol
Keywords = alcohol-related birth defects
Keywords = FAS
Keywords = genetic susceptibility
Lot batch = SD255

source_name: 2.9 g/kg ethanol headfold at 3.0h

source_name: saline - control headfold, C57BL/6N


title: EtOH: PK11195 in C57BL/6N mice

description:
Date :	12/29/2002
Original sample
Species :	Mouse
Strain :	C57BL/6N
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	ethanol
Route :	single i.p. injection
Dose :	2.9 g/kg
Time :	3 hrs post-injection
Intervention :	4.0 mg/kg PK11195 co-administered
Risk: no increased risk for malformation anticipated
Conditional biomarker: no p53 protein induction observed
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = ethanol
Keywords = alcohol-related birth defects
Keywords = FAS
Keywords = genetic susceptibility
Keywords = PK11195
Lot batch = SD332


title: EtOH: Ro5-4864 in C57BL/6J mice

description:
Date :	2/4/2003
Original sample
Species :	Mouse
Strain :	C57BL/6J
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	ethanol
Route :	single i.p. injection
Dose :	2.9 g/kg
Time :	3 hrs post-injection
Intervention :	4.0 mg/kg Ro5-4864 co-administered
Risk: unknown
Conditional biomarker: no p53 protein induction observed
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = ethanol
Keywords = alcohol-related birth defects
Keywords = FAS
Keywords = genetic susceptibility
Keywords = Ro5-4864
Lot batch = SD762


title: EtOH: Ro5-4864 in C57BL/6J mice

description:
Date :	1/22/2003
Original sample
Species :	Mouse
Strain :	C57BL/6J
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	ethanol
Route :	single i.p. injection
Dose :	2.9 g/kg
Time :	3 hrs post-injection
Intervention :	4.0 mg/kg Ro5-4864 co-administered
Risk: unknown
Conditional biomarker: no p53 protein induction observed
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = ethanol
Keywords = alcohol-related birth defects
Keywords = FAS
Keywords = genetic susceptibility
Keywords = Ro5-4864
Lot batch = SE251


title: EtOH: C57BL/6N headfold at 3.0h

description:
Date :	9/5/2002
Original sample
Species :	Mouse
Strain :	C57BL/6N
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	ethanol
Route :	single i.p. injection
Dose :	2.9 g/kg
Time :	3 hrs post-injection
Intervention :	none
Risk: no increased risk for malformations
Conditional biomarker: weak p53 protein induction
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = ethanol
Keywords = alcohol-related birth defects
Keywords = FAS
Keywords = genetic susceptibility
Lot batch = SD254


title: Ro5-4864: PK11195 intervention

description:
Date	2/15/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	Ro5-4864
Route :	single i.p. injection
Dose :	4.0 mg/kg
Time :	4.5 hrs post-injection
Intervention :	4.0 mg/kg
PK11195 co-administered
Risk: 20% increased risk of microphthalmia
Conditional biomarker: not tested
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = PK11195
Keywords = Ro5-4864
Keywords = embryo
Lot batch = SA958

source_name: 4.0 mg/kg Ro5-4864 headfold at 4.5h

source_name: 4.0 mg/kg PK11195 headfold at 4.5h


title: Ro5-4864: PK11195 intervention

description:
Date	2/15/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	Ro5-4864
Route :	single i.p. injection
Dose :	4.0 mg/kg
Time :	4.5 hrs post-injection
Intervention :	4.0 mg/kg PK11195 co-administered
Risk: 20% increased risk of microphthalmia
Conditional biomarker: not tested
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = PK11195
Keywords = Ro5-4864
Keywords = embryo
Lot batch = SA959


title: EtOH at 3.0h in C57BL/6J mice

description:
Date :	1/21/2003
Original sample
Species :	Mouse
Strain :	C57BL/6J
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	ethanol
Route :	single i.p. injection
Dose :	2.9 g/kg
Time :	3 hrs post-injection
Intervention :	none
Risk: <20% estimated risk for alcohol-related birth defects
Conditional biomarker: no p53 protein induction observed
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = ethanol
Keywords = alcohol-related birth defects
Keywords = FAS
Keywords = genetic susceptibility
Lot batch = SE256

source_name: saline - control headfold, C57BL/6J


title: 2CdA: Ro5-4864 headfold at 4.5h

description:
Date	1/21/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	2-chloro-2'-deoxyadenosine
Route :	single i.p. injection
Dose :	2.5 mg/kg
Time :	4.5 hrs post-injection
Intervention :	4.0 mg/kg Ro5-4864 co-administered
Risk: 25% increased risk for microphthalmia
Conditional biomarker: p53 protein induction
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = 2-chlorodeoxyadenosine
Keywords = Ro5-4864
Keywords = embryo
Keywords = microphthalmia
Lot batch = SA933

source_name: 2.5 mg/kg 2CdA + Ro5-4864 headfold

source_name: 2CdA treated headfold


title: 2CdA: Ro5-4864 headfold at 4.5h

description:
Date	1/21/2002
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	headfold
Treatments applied
Agent :	2-chloro-2'-deoxyadenosine
Route :	single i.p. injection
Dose :	2.5 mg/kg
Time :	4.5 hrs post-injection
Intervention :	4.0 mg/kg Ro5-4864 co-administered
Risk: 25% increased risk for microphthalmia
Conditional biomarker: p53 protein induction
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	16-20 headfolds pooled from two litters
Hybridization extract preparation :	2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103)
Labeling (cDNA) :	fluorescein-12-dCTP, biotinyl-11-dCTP
Hybridization condition :	56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC
Detection & raw data organization
Immunodetection :	anti-FL with Cy3-tyramide,  peroxidase-conjugated streptavidin with Cy5-tyramide
Scanning :	Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm
Spot measurement :	ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot).
Background correction :	The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately.
Gene expression matrix :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = 2-chlorodeoxyadenosine
Keywords = Ro5-4864
Keywords = embryo
Keywords = microphthalmia
Lot batch = SA923