title: MGMH030311039Atrachea

description: trachea


title: MGJZ030207020Alymphnode

status: Public on Mar 19 2004

type: RNA

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

country: USA

institute: Genomics Institute of the Novartis Research Foundation

description: lymphnode; mesenteric

molecule: total RNA

organism: Mus musculus


title: MGJZ030207041Buterus

description: uterus


title: MGJZ030211071Adorsalstriatum

description: dorsal striatum; above anterior commisure, approximately Bregma 1.3 to -0.3


title: MGMH030211026Aretina

description: retina


title: MGMH030212040Btrigeminal

description: trigeminal


title: MGJZ030228080Bpituitary

description: pituitary


title: MGMH030211026Bretina

description: retina


title: MGMH030211062Bamygdala

description: amygdala


title: MGJZ030207007Bcerebellum

description: cerebellum


title: MGMH030212040Atrigeminal

description: trigeminal


title: MGJZ030228080Apituitary

description: pituitary


title: MGJZ030207007Acerebellum

description: cerebellum


title: MGMH030311039Btrachea

description: trachea


title: MGJZ030312065Adorsalrootganglion

description: dorsal root ganglion


title: MGJZ030207020Blymphnode

description: lymphnode; mesenteric


title: MGJZ030207041Auterus

description: uterus


title: MGJZ030212070Aolfactorybulb

description: olfactory bulb


title: MGJZ030212070Bolfactorybulb

description: olfactory bulb


title: MGMH030211062Aamygdala

description: amygdala; approximately Bregma -1.1 to -2.1


title: MGJZ030212014Ahippocampus

description: hippocampus


title: MGJZ030212014Bhippocampus

description: hippocampus


title: MGJZ030312065Bdorsalrootganglion

description: dorsal root ganglion


title: MGJZ030212008Bcerebralcortex

description: cerebral cortex; minus frontal


title: MGMH030312008Acortex

description: cerebral cortex


title: MGJZ030211071Bdorsalstriatum


title: MGMH030212053Bhypothalamus

description: hypothalamus


title: MGMH030212057Aspinalcordlower

description: spinal cord lower; lower half


title: MGJZ030212009Bfrontalcortex

description: frontal cortex


title: MGMH030212053Ahypothalamus

description: hypothalamus


title: MGMH030401094Apreoptic

description: preoptic


title: MGJZ030212009Afrontalcortex

description: frontal cortex


title: MGMH030402094Bpreoptic

description: preoptic


title: MGJZ030212072Bsubstantianigra

description: substantia nigra


title: MGMH030212058Aspinalcordupper

description: spinal cord upper; upper half


title: MGMH030212057Bspinalcordlower

description: spinal cord lower; lower half


title: Rosiglitazone-2

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

description: Pooled aortic mRNA isolated from adult male mice (C57BL/6J strain) treated for 21 days with a PPAR gamma agonist (rosiglitazone, 25 mg/kg/day).

source_name: Total RNA from mouse aorta


title: Vehicle-3

description: Pooled aortic mRNA isolated from adult male mice (C57BL/6J strain) treated for 21 days with vehicle.


title: Rosiglitazone-1


title: MGMH030212058Bspinalcordupper

description: spinal cord upper; upper half


title: 3025H: ExpB-Histogram-KOrep1cy3-HCT116rep1cy5

status: Public on Mar 16 2004

city: Cambridge

first: Ahmed

middle: Ashour

last: Ahmed

address: Robinson Way

department: Oncology, University of Cambridge

country: United Kingdom

institute: Cancer Research UK Cambridge Research Institute

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (15 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy3 and Cy5 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the histogram method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300

organism: Homo sapiens

source_name: KO


title: MGJZ030212072Asubstantianigra

description: substantia nigra


title: 3033H: ExpB-Histogram-KOrep2cy3-HCT116rep2cy5


title: 3034H: ExpB-Histogram-KOrep4cy5-HCT116rep4cy3

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (15 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the histogram method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3069H: ExpA-Histogram-KOrep6cy5-HCT116rep6cy3

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (10 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the histogram method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3097H: ExpA-Histogram-KOrep3cy3-HCT116rep3cy5

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (10 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy3 and Cy5 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the histogram method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: Vehicle-4


title: 3092H: ExpA-Histogram-KOrep4cy5-HCT116rep4cy3


title: 3054H: ExpB-Histogram-KOrep3cy3-HCT116rep3cy5


title: 3036H: ExpB-Histogram-KOrep5cy5-HCT116rep5cy3


title: 3037H: ExpB-Histogram-KOrep6cy5-HCT116rep6cy3


title: 3093H: ExpA-Histogram-KOrep5cy5-HCT116rep5cy3


title: 3084H: ExpA-Histogram-KOrep1cy3-HCT116rep1cy5


title: 3036G: ExpB-Genepix-KOrep5cy5-HCT116rep5cy3

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (15 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the GenePix Pro 4.1 (Axon Instruments, Inc.) software. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3089H: ExpA-Histogram-KOrep2cy3-HCT116rep2cy5


title: 3025G: ExpB-Genepix-KOrep1cy3-HCT116rep1cy5

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (15 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy3 and Cy5 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the GenePix Pro 4.1 (Axon Instruments, Inc.) software. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3034G: ExpB-Genepix-KOrep4cy5-HCT116rep4cy3


title: 3097G: ExpA-Genepix-KOrep3cy3-HCT116rep3cy5

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (10 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy3 and Cy5 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the GenePix Pro 4.1 (Axon Instruments, Inc.) software. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3069G: ExpA-Genepix-KOrep6cy5-HCT116rep6cy3

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (10 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the GenePix Pro 4.1 (Axon Instruments, Inc.) software. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3054G: ExpB-Genepix-KOrep3cy3-HCT116rep3cy5


title: testis tubular somatic cells replicate 1 GPL81

city: New York

first: Nikolaus

last: Schultz

state: NY

address: 1275 York Ave, Box 460

department: Computational Biology Center

institute: Memorial Sloan-Kettering Cancer Center

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 0.918).
Keywords = Mus musculus, testis, spermatogenesis

source_name: 19 day old testis, tubular somatic cells


title: testis laminin non-binding germ cells replicate 2 GPL81

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 1.346).
Keywords = Mus musculus, testis, spermatogenesis

source_name: 19 day old testis, cultured germ cells


title: 3089G: ExpA-Genepix-KOrep2cy3-HCT116rep2cy5


title: 3025F: ExpB-Fixed circle-KOrep1cy3-HCT116rep1cy5

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (15 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy3 and Cy5 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the fixed circle method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3037G: ExpB-Genepix-KOrep6cy5-HCT116rep6cy3

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (15 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the GenePix Pro 4.1 (Axon Instruments, Inc.) softwarey. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3033G: ExpB-Genepix-KOrep2cy3-HCT116rep2cy5


title: 3037F: ExpB-Fixed circle-KOrep6cy5-HCT116rep6cy3

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (15 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the fixed circle method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3093F: ExpA-Fixed circle-KOrep5cy5-HCT116rep5cy3

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (10 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the fixed circle method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3033F: ExpB-Fixed circle-KOrep2cy3-HCT116rep2cy5


title: 3093G: ExpA-Genepix-KOrep5cy5-HCT116rep5cy3


title: 3036F: ExpB-Fixed circle-KOrep5cy5-HCT116rep5cy3


title: laminin binding germ cells GPL341

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 1.028).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis

organism: Rattus norvegicus

source_name: germ cells from 22 day old rat testis, cultured


title: testis laminin binding germ cells replicate 2 GPL81

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 2.221).
Keywords = Mus musculus, testis, spermatogenesis


title: 3034F: ExpB-Fixed circle-KOrep4cy5-HCT116rep4cy3


title: 3069F: ExpA-Fixed circle-KOrep6cy5-HCT116rep6cy3


title: 3092G: ExpA-Genepix-KOrep4cy5-HCT116rep4cy3


title: testis laminin non-binding germ cells replicate 1 GPL81

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 1.257).
Keywords = Mus musculus, testis, spermatogenesis


title: 3097F: ExpA-Fixed circle-KOrep3cy3-HCT116rep3cy5

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (10 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy3 and Cy5 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the fixed circle method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3089F: ExpA-Fixed circle-KOrep2cy3-HCT116rep2cy5


title: 3084F: ExpA-Fixed circle-KOrep1cy3-HCT116rep1cy5


title: 3037A: ExpB-Adaptive-KOrep6cy5-HCT116rep6cy3

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (15 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the adaptive method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3084G: ExpA-Genepix-KOrep1cy3-HCT116rep1cy5


title: 3054F: ExpB-Fixed circle-KOrep3cy3-HCT116rep3cy5


title: 3092F: ExpA-Fixed circle-KOrep4cy5-HCT116rep4cy3


title: laminin non-binding germ cells GPL341

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 0.582).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis


title: testis tubular somatic cells GPL341

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 0.584).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis

source_name: 22 day old testis, tubular somatic cells


title: testis laminin binding germ cells replicate 1 GPL81

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 1.312).
Keywords = Mus musculus, testis, spermatogenesis


title: 3036A: ExpB-Adaptive-KOrep5cy5-HCT116rep5cy3


title: germ cells on STO day 20 GPL341

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 0.670).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis

source_name: germ cells from 22 day old rat testis, cultured for 20 days


title: testis interstitial cells GPL341

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 0.391).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis

source_name: 22 day old testis, interstitial cells


title: testis tubular somatic cells replicate 1 GPL83

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 3.818).
Keywords = Mus musculus, testis, spermatogenesis


title: testis laminin non-binding germ cells replicate 2 GPL83

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 4.984).
Keywords = Mus musculus, testis, spermatogenesis


title: testis laminin non-binding germ cells  replicate 1 GPL83

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 3.030).
Keywords = Mus musculus, testis, spermatogenesis


title: germ cells on STO day 1 GPL341

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 0.510).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis

source_name: germ cells from 22 day old rat testis, cultured for 1 day


title: germ cells on STO day 5 GPL341

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 1.512).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis

source_name: germ cells from 22 day old rat testis, cultured for 5 days


title: testis tubular somatic cells GPL342

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 3.274).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis


title: laminin binding germ cells GPL342

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 4.009).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis


title: germ cells on STO day 20 GPL342

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 1.441).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis


title: germ cells on STO day 10 GPL341

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 0.660).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis

source_name: germ cells from 22 day old rat testis, cultured for 10 days


title: 3034A: ExpB-Adaptive-KOrep4cy5-HCT116rep4cy3


title: testis laminin binding germ cells replicate 2 GPL83

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 4.498).
Keywords = Mus musculus, testis, spermatogenesis


title: 3033A: ExpB-Adaptive-KOrep2cy3-HCT116rep2cy5

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (15 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy3 and Cy5 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the adaptive method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: germ cells on MSC1 day 20 GPL341

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 1.098).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis


title: testis interstitial cells GPL342

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 1.047).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis


title: laminin non-binding germ cells GPL342

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 2.117).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis


title: testis laminin binding germ cells replicate 1 GPL83

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 3.444).
Keywords = Mus musculus, testis, spermatogenesis


title: testis tubular somatic cells replicate 1 GPL82

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 3.130).
Keywords = Mus musculus, testis, spermatogenesis


title: testis laminin non-binding germ cells replicate 2 GPL82

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 2.953).
Keywords = Mus musculus, testis, spermatogenesis


title: 3054A: ExpB-Adaptive-KOrep3cy3-HCT116rep3cy5


title: germ cells on STO day 5 GPL342

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 3.834).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis


title: germ cells on STO day 1 GPL342

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 1.546).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis


title: 3069A: ExpA-Adaptive-KOrep6cy5-HCT116rep6cy3

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (10 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the adaptive method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: 3025A: ExpB-Adaptive-KOrep1cy3-HCT116rep1cy5


title: 3092A: ExpA-Adaptive-KOrep4cy5-HCT116rep4cy3


title: RET1907Pv41

city: Memphis

first: Michael

last: Dyer

state: TN

address: 332 N Lauderdale

institute: St Jude

description:
Rb knockout retina
Type:GenePix Results 3
DateTime:2003/08/08 10:16:17
PixelSize:10
Wavelengths:635	532
NormalizationMethod:None
NormalizationFactors:1	1
JpegImage:W:\to_be\Ret1907P.jpg
StdDev:Type 1
RatioFormulations:W1/W2 (635/532)
Barcode:
BackgroundSubtraction:LocalFeature
ImageOrigin:1040, 4080
JpegOrigin:1120, 4080
Creator:GenePix Pro 4.1.1.29
Scanner:GenePix 4000B [84596]
FocusPosition:0
NormalizationFactor:RatioOfMedians:1.865660631241
NormalizationFactor:RatioOfMeans:1.91286734200691
NormalizationFactor:MedianOfRatios:1.8500338697383
NormalizationFactor:MeanOfRatios:1.89540568351896
NormalizationFactor:RegressionRatio:1.91070820108598
NormalizationFactor:ArabidopsisRatioOfMedians:1.24490872924588
Temperature:38.35
LinesAveraged:1
Comment:
PMTGain:890	730
ScanPower:100	100
LaserPower:3.34	3.82
LaserOnTime:69445	52018
Filters:<Empty>	<Empty>
ScanRegion:104,408,1988,5760
Supplier:
Keywords = Rb,retina blastoma

source_name: Wild Type mice

source_name: mutant mice (Rb-)


title: germ cells on MSC1 day 20 GPL342

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 3.100).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis


title: 3093A: ExpA-Adaptive-KOrep5cy5-HCT116rep5cy3


title: germ cells on STO day 10 GPL342

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 1.464).
Keywords = Rat, testis, germ cells, stem cells, spermatogenesis


title: testis laminin binding germ cells replicate 2 GPL82

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 3.076).
Keywords = Mus musculus, testis, spermatogenesis


title: testis laminin non-binding germ cells replicate 1 GPL82

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 1.957).
Keywords = Mus musculus, testis, spermatogenesis


title: 3097A: ExpA-Adaptive-KOrep3cy3-HCT116rep3cy5

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (10 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy3 and Cy5 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the adaptive method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116, KO, EP300


title: NSH ESTs (LBG Rep 1)

status: Public on Mar 14 2004

city: Stillwater

first: Patricia

middle: J

last: Ayoubi-Canaan

state: OK

address: 246 Noble Research Center

department: Biochemistry and Molecular Biology

institute: Oklahoma State University

description:
RNA was isolated from lyophilized cultures of Aspergillus nidulans (RMS11) grown on 1% locust bean gum (LBG) using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer.
Keywords = NSH
Keywords = subtraction
Keywords = aspergillus
Keywords = polysaccharide
Keywords = exopolygalacturonase

organism: Aspergillus nidulans

source_name: Aspergillus nidulans grown on 1% LBG


title: NSH ESTs (LBG Rep 3)


title: NSH-ESTs (Glucose Rep 2)

status: Public on Mar 15 2004

description:
RNA was isolated from lyophilized cultures of Aspergillus nidulans (RMS11) grown on 1% glucose using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer.

Keywords = NSH
Keywords = subtraction
Keywords = aspergillus
Keywords = polysaccharide
Keywords = exopolygalacturonase

source_name: Aspergillus nidulans grown on 1% glucose


title: NSH ESTs (LBG Rep 2)


title: RET1906Pv41

description:
Rb knockout retina
Type:GenePix Results 3
DateTime:2003/08/08 10:06:27
PixelSize:10
Wavelengths:635	532
NormalizationMethod:None
NormalizationFactors:1	1
JpegImage:W:\to_be\RET1906P.jpg
StdDev:Type 1
RatioFormulations:W1/W2 (635/532)
Barcode:
BackgroundSubtraction:LocalFeature
ImageOrigin:1000, 4120
JpegOrigin:1270, 4180
Creator:GenePix Pro 4.1.1.29
Scanner:GenePix 4000B [84596]
FocusPosition:0
NormalizationFactor:RatioOfMedians:0.912931438242543
NormalizationFactor:RatioOfMeans:0.943735156184071
NormalizationFactor:MedianOfRatios:0.930160047415823
NormalizationFactor:MeanOfRatios:0.918537202516803
NormalizationFactor:RegressionRatio:0.927361793120605
NormalizationFactor:ArabidopsisRatioOfMedians:1.67417671469535
Temperature:38.29
LinesAveraged:1
Comment:
PMTGain:840	730
ScanPower:100	100
LaserPower:3.34	3.82
LaserOnTime:69435	52008
Filters:<Empty>	<Empty>
ScanRegion:100,412,1984,5800
Supplier:
Keywords = Rb,retina blastoma


title: testis laminin binding germ cells replicate 1 GPL82

description:
50 ng total RNA were amplified using two rounds of amplification. Detection calls were calculated using a Tau value of 0.015. Signal intensities were scaled to an average of 250 (scale factor 2.304).
Keywords = Mus musculus, testis, spermatogenesis


title: NSH ESTs (Arabinan Rep 1)

description:
RNA was isolated from lyophilized cultures of Aspergillus nidulans (RMS11) grown on 1% arabinan using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer.
Keywords = NSH
Keywords = subtraction
Keywords = aspergillus
Keywords = polysaccharide
Keywords = exopolygalacturonase

source_name: Aspergillus nidulans grown on 1% arabinan


title: NSH ESTs (Gum arabic Rep 3)

description:
RNA was isolated from lyophilized cultures of Aspergillus nidulans (RMS11) grown on 1% gum arabic using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer.
Keywords = NSH
Keywords = subtraction
Keywords = aspergillus
Keywords = polysaccharide
Keywords = exopolygalacturonase

source_name: Aspergillus nidulans grown on 1% Gum arabic


title: NSH ESTs (Gum arabic Rep 1)


title: RET1902Pv41

description:
Rb knockout retina
Type:GenePix Results 3
DateTime:2003/08/08 09:58:11
PixelSize:10
Wavelengths:635	532
NormalizationMethod:None
NormalizationFactors:1	1
JpegImage:W:\to_be\RET1902P.jpg
StdDev:Type 1
RatioFormulations:W1/W2 (635/532)
Barcode:
BackgroundSubtraction:LocalFeature
ImageOrigin:1040, 3840
JpegOrigin:1040, 3960
Creator:GenePix Pro 4.1.1.29
Scanner:GenePix 4000B [84596]
FocusPosition:10
NormalizationFactor:RatioOfMedians:1.60421386511316
NormalizationFactor:RatioOfMeans:1.6461121545244
NormalizationFactor:MedianOfRatios:1.60258361808825
NormalizationFactor:MeanOfRatios:1.62058587381104
NormalizationFactor:RegressionRatio:1.65173080302232
NormalizationFactor:ArabidopsisRatioOfMedians:1.12171866808101
Temperature:38.23
LinesAveraged:1
Comment:
PMTGain:860	730
ScanPower:100	100
LaserPower:3.34	3.81
LaserOnTime:69427	52000
Filters:<Empty>	<Empty>
ScanRegion:104,384,1988,5772
Supplier:
Keywords = Rb,retina blastoma


title: NSH ESTs (Gum arabic Rep 2)


title: RET1900Pv41

description:
Rb knockout retina
Type:GenePix Results 3
DateTime:2003/08/08 09:22:37
PixelSize:10
Wavelengths:635	532
NormalizationMethod:None
NormalizationFactors:1	1
JpegImage:W:\to_be\RET1900P.jpg
StdDev:Type 1
RatioFormulations:W1/W2 (635/532)
Barcode:
BackgroundSubtraction:LocalFeature
ImageOrigin:1040, 3840
JpegOrigin:1140, 4030
Creator:GenePix Pro 4.1.1.29
Scanner:GenePix 4000B [84596]
FocusPosition:10
NormalizationFactor:RatioOfMedians:1.37918870002311
NormalizationFactor:RatioOfMeans:1.42947734912954
NormalizationFactor:MedianOfRatios:1.39385161428946
NormalizationFactor:MeanOfRatios:1.40794178845986
NormalizationFactor:RegressionRatio:1.41316954605509
NormalizationFactor:ArabidopsisRatioOfMedians:0.860285907784672
Temperature:37.71
LinesAveraged:1
Comment:
PMTGain:880	730
ScanPower:100	100
LaserPower:3.35	3.8
LaserOnTime:69391	51965
Filters:<Empty>	<Empty>
ScanRegion:104,384,1988,5752
Supplier:
Keywords = Rb,retina blastoma


title: NSH-ESTs (Pectin Rep 2)

description:
RNA was isolated from lyophilized cultures of Aspergillus nidulans (RMS11) grown on 1% pectin using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer.
Keywords = NSH
Keywords = subtraction
Keywords = aspergillus
Keywords = polysaccharide
Keywords = exopolygalacturonase

source_name: Aspergillus nidulans grown on 1% pectin


title: NSH ESTs (Pectin Rep 3)


title: NSH-ESTs (Pectin Rep 1)

description:
RNA was isolated from lyophilized cultures of Aspergillus nidulans (RMS11) grown on 1% pectin using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer
Keywords = NSH
Keywords = subtraction
Keywords = aspergillus
Keywords = polysaccharide
Keywords = exopolygalacturonase


title: NSH ESTs (Arabinan Rep 3)


title: NSH ESTs (Arabinan Rep 2)


title: 3084A: ExpA-Adaptive-KOrep1cy3-HCT116rep1cy5

description:
Human HCT116 cell line and an EP300 knock-out HCT116 line (KO) were grown in McCoy's medium containing  10% fetal calf serum. The experiment was done to compare the expression differences between the parent HCT116 cell line and the derived KO cell line.
Cells were plated in T75 flasks. They were cultured until they were 80% confluent and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with the Tri-Reagent (SIgma) and purified using the Qiagen RNeasy Mini Kit reagents. The  RNA (10 ug) was annealed with a random hexamer primer, and reverse-transcribed into cDNA with Powerscript (Clontech) reverse transcriptase for 2h at 42 degrees in the presence of  amino-allyl dUTP.
The cDNA from KO RNA and HCT116 RNA was covalently coupled separately with Cy3 and Cy5 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy3 and Cy5 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and  hybridized to the microarray using the Hybrite chamber (Vysis).
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray 4000 (Perkin Elmer) at a resolution of 10 um at maximum laser power and photo-multiplier tube voltage of 50 to 60%. Segmentation was performed using the adaptive method of the QuantArray (Perkin Elmer) package. Data was transformed into log base 2 expression ratios and normalized using scaled loess normalization.
Keywords = HCT116
Keywords = KO
Keywords = EP300

source_name: KO


title: 3089A: ExpA-Adaptive-Korep2cy3-HCT116rep2cy5


title: NSH-ESTs (CMC Rep 2)

description:
RNA was isolated from lyophilized cultures of Aspergillus nidulans (RMS11) grown on 1% carboxy methyl cellulose (CMC) using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer
Keywords = NSH
Keywords = subtraction
Keywords = aspergillus
Keywords = polysaccharide
Keywords = exopolygalacturonase

source_name: Aspergillus nidulans grown on 1% CMC


title: NSH ESTs (CMC Rep 3)

description:
RNA was isolated from lyophilized cultures of Aspergillus nidulans (RMS11) grown on 1% carboxy methyl cellulose using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer
Keywords = NSH
Keywords = subtraction
Keywords = aspergillus
Keywords = polysaccharide
Keywords = exopolygalacturonase


title: NSH-ESTs (CMC Rep 1)


title: NSH-ESTs (No Glucose Rep 2)

description:
RNA was isolated from lyophilized cultures of Aspergillus nidulans (RMS11) grown on Minimal media with no glucose using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer
Keywords = NSH
Keywords = subtraction
Keywords = aspergillus
Keywords = polysaccharide
Keywords = exopolygalacturonase

source_name: Aspergillus nidulans grown on Minimal media with no glucose


title: NSH-ESTs (No Glucose Rep 1)


title: RET1901Pv41

description:
Rb knockout retina
Type:GenePix Results 3
DateTime:2003/08/08 09:34:46
PixelSize:10
Wavelengths:635	532
NormalizationMethod:None
NormalizationFactors:1	1
JpegImage:W:\to_be\RET1901P.jpg
StdDev:Type 1
RatioFormulations:W1/W2 (635/532)
Barcode:
BackgroundSubtraction:LocalFeature
ImageOrigin:1040, 3840
JpegOrigin:1240, 4190
Creator:GenePix Pro 4.1.1.29
Scanner:GenePix 4000B [84596]
FocusPosition:10
NormalizationFactor:RatioOfMedians:1.01095636269871
NormalizationFactor:RatioOfMeans:1.04627991686217
NormalizationFactor:MedianOfRatios:1.02540089383809
NormalizationFactor:MeanOfRatios:1.02214189668477
NormalizationFactor:RegressionRatio:0.989488140726324
NormalizationFactor:ArabidopsisRatioOfMedians:2.47472620050548
Temperature:37.98
LinesAveraged:1
Comment:
PMTGain:860	730
ScanPower:100	100
LaserPower:3.35	3.81
LaserOnTime:69404	51977
Filters:<Empty>	<Empty>
ScanRegion:104,384,1988,5772
Supplier:
Keywords = Rb,retina blastoma


title: NSH-ESTs (Glucose Rep 3)

description:
RNA was isolated from lyophilized cultures of Aspergillus nidulans (RMS11) grown on 1% glucose using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer
Keywords = NSH
Keywords = subtraction
Keywords = aspergillus
Keywords = polysaccharide
Keywords = exopolygalacturonase


title: NSH-ESTs (Glucose Rep 1)

description:
RNA was isolated from lyophilized cultures of Aspergillus nidulans (RMS11) grown on 1% glucose using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using the 3DNA detection system from Genisphere (Hatfield, PA) as recommended by the manufacturer.
Keywords = NSH
Keywords = subtraction
Keywords = aspergillus
Keywords = polysaccharide
Keywords = exopolygalacturonase


title: NSH-ESTs (No Glucose Rep 3)


title: 72 h serum-deprived T98G cells with 1 h U0126 and 30 min PDGF treatments, replicate 1

status: Public on Mar 13 2004

city: Boston

first: Geoffrey

middle: M

last: Cooper

state: MA

address: 5 Cummington St

department: Biology

institute: Boston University

description: T98G human glioblastoma cells were grown in Minimal Essential Medium (Invitrogen) supplemented with fetal calf serum (10%). For growth factor/inhibitor treatments, cells were incubated in serum-free medium for 72 h, and either left unstimulated, or stimulated for 30 min with human PDGF-BB (50 ng/ml) (Sigma). U0126 (Cell Signaling Technology) and LY294002 (BioMol) were added 60 min prior to PDGF addition.

source_name: 72hr serum starved T98G cells (untreated)


title: aRMS 3268

city: Heidelberg

first: Matthias

last: Nees

address: Im Neuenheimer Feld 156

department: Pediatric Oncology & Hematology

country: Germany

institute: Heidelberg University, Children's Hospital

description: Primary paediatric rhabdomyosarcoma biopsy, alveolar histology

source_name: alveolar rhabdomyosarcoma


title: 72 h serum-deprived T98G cells with 30 min PDGF treatment, replicate 5


title: 72 h serum-deprived T98G cells with 30 min PDGF treatment, replicate 4


title: aRMS 3003


title: aRMS 1063


title: aRMS 2016


title: 72 h serum-deprived T98G cells with 1 h LY294002 + U0126 and 30 min PDGF treatments, replicate 1


title: 72 h serum-deprived T98G cells with 30 min PDGF treatment, replicate 1


title: eRMS 321

description: Primary paediatric rhabdomyosarcoma biopsy, embryonal histology

source_name: embryonal rhabdomyosarcoma


title: aRMS 1119


title: aRMS 1403


title: aRMS 1103


title: 72 h serum-deprived T98G cells with 30 min PDGF treatment, replicate 2


title: 72 h serum-deprived T98G cells with 30 min PDGF treatment, replicate 3


title: eRMS 1249


title: aRMS 1776


title: 72 h serum-deprived T98G cells with 1 h LY294002 and 30 min PDGF treatments, replicate 1


title: 72 h serum-deprived T98G cells with 1 h LY294002 + U0126 and 30 min PDGF treatments, replicate 2


title: eRMS 753


title: 72 h serum-deprived T98G cells with 1 h LY294002 and 30 min PDGF treatments, replicate 2


title: 72 h serum-deprived T98G cells with 1 h U0126 and 30 min PDGF treatments, replicate 2


title: EWS 98

description: Primary paediatric Ewing's sarcoma biopsy

source_name: Ewing's sarcoma


title: EWS 95


title: EWS 687


title: EWS 91


title: EWS 520


title: EWS 1956


title: EWS 1764


title: EWS 160


title: aRMS 1814


title: DITPA-1

status: Public on Mar 12 2004

city: Copenhagen

first: Claes

middle: C

last: Strøm

address: 20, Juliane Mariesvej

department: Department of Medicine B

country: Denmark

institute: H:S Rigshospitalet, University of Copenhagen Medical School

description:
left ventricle 2 weeks after s.c. infusion of the thyroxin analogue 3,5-diiodothyropropionic acid
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy

source_name: heart left ventricle


title: EWS 1267


title: ANG2-2

description:
left ventricle 2 weeks after s.c. infusion of angiotensin 2
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: NEO-1

description:
neonatal left ventricle
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: ANG2-1


title: DITPA-2


title: NEO-2


title: EWS 1374


title: AB30-2

description:
left ventricle 30 weeks after ascending aortic banding
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: AB30-4


title: VEH-1

description:
left ventricle 2 weeks after s.c. infusion of saline
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: AB30-3


title: Galactose response of Saccharomyces cerevisiae

city: New Haven

first: Kevin

last: McConnell

state: CT

address: 2 Church Street South, Suite 401

institute: Agilix Corporation

description:
Analysis of expression changes in Saccharomyces cerevisiae strain XS1385-8 in response to galactose induction using Universal Microarray System.
For complete protocol details, see Roth et al. Nature Biotechnology (2004).
Keywords = Saccharomyces cerevisiae, galactose, glucose, umas, GenCompass

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae XS1385-8A grown in glucose media<->S. cerevisiae XS1385-8A grown in galactose media


title: AB30-1


title: et-1 treated

city: London

first: Andrew

last: Leask

institute: Royal Free and University College Medical School

description: primary lung fibroblasts p3 from normal periphery of resected cancer. grown in DMEM 10% FBS, until confluence, then DMEM 0.5% FBS for 18 hours. Media were then changed and incubated for an additional 4 hours with 100 nM endothelin-1 (ET-1)

source_name: human primary lung fibroblasts


title: AB30-6

description:
left ventricle 30 weeks after ascending aortic banding - sham operated
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: VEH-2


title: AB30-5


title: AB16-1

description:
left ventricle 16 weeks after ascending aortic banding
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: AB16-4

description:
left ventricle 16 weeks after ascending aortic banding - sham operated
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: AB12-1

description:
left ventricle 12 weeks after ascending aortic banding
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: AB12-4

description:
left ventricle 12 weeks after ascending aortic banding - sham operated
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: untreated

description: primary lung fibroblasts p3 from normal periphery of resected cancer. grown in DMEM 10% FBS, until confluence, then DMEM 0.5% FBS for 18 hours. Media were then changed and incubated for an additional 4 hours

source_name: human lung fibroblasts (primary cells)


title: AB16-2


title: EWS 232


title: AB16-3


title: AB12-2


title: MI9-3

description:
left ventricle 9 weeks after myocardial infarction
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: AB12-3


title: AB6-4

description:
left ventricle 6 weeks after ascending aortic banding - sham operated
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: MI3-2

description:
left ventricle 3 weeks after myocardial infarction - sham operated
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: MI9-1


title: MI9-2


title: MI9-4


title: MI3-3

description:
left ventricle 3 weeks after myocardial infarction
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: S8-1

description:
left ventricle after 8 weeks of volume overload by an av-fistula
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: AB6-3


title: MI3-6


title: AB6-2

description:
left ventricle 6 weeks after ascending aortic banding
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: MI9-6

description:
left ventricle 9 weeks after myocardial infarction - sham operated
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: MI3-5


title: MI9-5


title: AB6-1


title: S8-2


title: MI3-4


title: MI3-1


title: S8-4

description:
left ventricle after 8 weeks of volume overload by an av-fistula - sham operated
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: S3-4

description:
left ventricle after 3 weeks of volume overload by an av-fistula - sham operated
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: optic vesicle stage in rat

status: Public on Mar 11 2004

city: Louisville

first: Thomas

middle: B

last: Knudsen

state: KY

address: 501 S Preston St

department: Birth Defects Center

institute: University of Louisville

description:
Date :	8/28/2002
Original sample
Species :	Rat
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	10.5 d.p.c.
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 :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = eye development
Keywords = embryo
Keywords = rat
Lot batch = SC295

source_name: optic vesicle, rat embryos

source_name: headfold, rat embryo at 9.5 d.p.c.


title: optic vesicle stage in rat

description:
Date :	8/28/2002
Original sample
Species :	Rat
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	10.5 d.p.c.
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 :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = eye development
Keywords = embryo
Keywords = rat
Lot batch = SC296


title: optic cup stage in rat

description:
Date :	8/28/2002
Original sample
Species :	Rat
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	11.0 d.p.c.
Tissue :	optic cup
Treatments applied
Agent :	none
Route :	none
Dose :	none
Time :	28-32 somite stage
Intervention :	noneRisk: none
Conditional biomarker: p53 protein induction not observed or anticipated
Technical extraction & labeling
Tissue procurement :	conventional microdissection
Sampling unit :	optic cups pooled from 27-30 embryos of 3 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 = eye development
Keywords = embryo
Keywords = rat
Lot batch = SD280

source_name: optic cup, rat embryos


title: S8-3


title: optic cup stage in rat

description:
Date :	8/28/2002
Original sample
Species :	Rat
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	11.0 d.p.c.
Tissue :	optic cup
Treatments applied
Agent :	none
Route :	none
Dose :	none
Time :	28-32 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 cups pooled from 27-30 embryos of 3 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 = eye development
Keywords = embryo
Keywords = rat
Lot batch = SD282


title: S3-1

description:
left ventricle after 3 weeks of volume overload by an av-fistula
Keywords = heart
Keywords = left ventricle
Keywords = hypertrophy


title: S3-3


title: S3-2


title: optic cup stage in mouse

description:
Date :	6/29/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	10 d.p.c., Theiler stage 16
Tissue :	optic cup
Treatments applied
Agent :	none
Route :	none
Dose :	none
Time :	28-32 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 cups pooled from 27-30 embryos of 3 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 = AN081

source_name: optic cup, mouse embryos

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


title: optic cup stage in mouse

description:
Date :	6/29/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	10 d.p.c., Theiler stage 16
Tissue :	optic cup
Treatments applied
Agent :	none
Route :	none
Dose :	none
Time :	28-32 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 cups pooled from 27-30 embryos of 3 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 = AN070


title: rat embryonic headfold

description:
Date :	8/28/2002
Original sample
Species :	Rat
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9.5 d.p.c.
Tissue :	headfold
Treatments applied
Agent :	none
Route :	none
Dose :	none
Time :	4-8 somite stage
Intervention :	none
Risk: none
Conditional biomarker: p53 protein induction not 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 :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = eye development
Keywords = embryo
Keywords = rat
Lot batch = SC638

source_name: rat headfold, 9.5 d.p.c.,sample A1

source_name: rat headfold, 9.5 d.p.c., sample A2


title: rat embryonic headfold

description:
Date :	8/28/2002
Original sample
Species :	Rat
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	9.5 d.p.c.
Tissue :	headfold
Treatments applied
Agent :	none
Route :	none
Dose :	none
Time :	4-8 somite stage
Intervention :	none
Risk: none
Conditional biomarker: p53 protein induction not 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 :	4800 element array less 36 control spots and averaging of duplicated elements resulting in 2382 spots

Keywords = eye development
Keywords = embryo
Keywords = rat
Lot batch = SC639


title: optic pit stage in mouse

description:
Date :	7/13/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	optic pit
Treatments applied
Agent :	none
Route :	none
Dose :	none
Time :	4-8 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 pits pooled from 48-50 embryos of 6 litters
Hybridization extract preparation :	1 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 = AN067

source_name: optic pit, mouse embryos


title: optic pit stage in mouse

description:
Date :	7/27/2001
Original sample
Species :	Mouse
Strain :	CD-1 (outbred)
Genotype :	wild-type
Stage :	8 d.p.c., Theiler stage 12
Tissue :	optic pit
Treatments applied
Agent :	none
Route :	none
Dose :	none
Time :	4-8 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 pits pooled from 48-50 embryos of 6 litters
Hybridization extract preparation :	1 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 = AN082


title: mouse embryonic headfold

description:
Date :	7/18/2001
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 = AN079

source_name: control headfold 8 d.p.c., sample A

source_name: control headfold 8 d.p.c., sample B


title: PK11195 in embryo culture at 2.0h

description:
Date :	6/6/2001
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 :	PK11195
Route :	whole embryo culture
Dose :	5.0 uM
Time :	2.0 hrs in culture
Intervention :	none
Risk: no increased risk for malformation
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 = AO094

source_name: forebrain from 21% oxygen at 2.0h


title: Ro5-4864 in embryo culture at 2.0h

description:
Date :	5/29/2001
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 :	Ro5-4864
Route :	whole embryo culture
Dose :	5.0 uM
Time :	2.0 hrs in culture
Intervention :	none
Risk: unknown
Conditional biomarker: unknown
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 = Ro5-4864
Keywords = microphthalmia
Lot batch = AO088


title: PK11195 in embryo culture at 2.0h

description:
Date :	6/6/2001
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 :	PK11195
Route :	whole embryo culture
Dose :	5.0 uM
Time :	2.0 hrs in culture
Intervention :	none
Risk: no increased risk for malformation
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 = AO093


title: Ro5-4864 in embryo culture at 2.0h

description:
Date :	5/29/2001
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 :	Ro5-4864
Route :	whole embryo culture
Dose :	5.0 uM
Time :	2.0 hrs in culture
Intervention :	none
Risk: unknown
Conditional biomarker: unknown
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 = Ro5-4864
Keywords = microphthalmia
Lot batch = AO087


title: Hypoxia: reoxygenation

description:
Date :	5/21/2001
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 = AM615

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

source_name: forebrain from 5% oxygen at 2.0h


title: optic vesicle stage in mouse

description:
Date :	6/25/2001
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 = AN089

source_name: optic vesicle, mouse embryos


title: Hypoxia: PK11195 intervention

description:
Date :	5/21/2001
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 = AM636

source_name: 5% oxygen + PK11195 at 2.0h


title: Hypoxia in embryo culture

description:
Date :	5/2/2001
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 :	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 = AM620