Human UniGene Set RZPD 1 - Zipf's Normalization
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE1510 | GEO | 2004/07/03
SECONDARY ACCESSION(S): PRJNA90839
REPOSITORIES: GEO
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Project description:Five microarrays from a larger dataset used to demonstrate a normalization technique base on Zipf's law. The original data set was generated by using Atlas Rat cDNA microarrays (Clontech, 588 genes) probed with rat brain tissue, from control (cerebellum n=10, olive n=10) and harmaline treated (cerebellum n=10, olive n=9) animals. Microarrays were probed according to established protocols and exposed to imaging plates overnight (BAS-MS 2325) and scanned at a 50 m resolution on a FLA-3000G phosphoimager (Raytest, Germany). Image gridding was carried out using VisualGrid® software (http://www.gpc-biotech.com). Keywords: other
2004-07-03 | GSE1509 | GEO
Project description:Five microarrays from a larger dataset used to demonstrate a normalization technique base on Zipf's law. The original data set was generated by using Atlas Rat cDNA microarrays (Clontech, 588 genes) probed with rat brain tissue, from control (cerebellum n=10, olive n=10) and harmaline treated (cerebellum n=10, olive n=9) animals. Microarrays were probed according to established protocols and exposed to imaging plates overnight (BAS-MS 2325) and scanned at a 50 m resolution on a FLA-3000G phosphoimager (Raytest, Germany). Image gridding was carried out using VisualGrid® software (http://www.gpc-biotech.com).
2010-06-06 | E-GEOD-1509 | biostudies-arrayexpress
Project description:I. Exp Design 1. Type of experiment: Comparison of native versus cultured RPE cells 2. Experimental factors: Native RPE versus ARPE-19 cells grown on different matrices 3. How many hybridizations in exp: 21 4. If a common reference used for all the hybs: no 5. Quality control steps: three independent arrays for each condition 6. Description: The expression profile of ARPE-19 cells grown on different matrices were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 3 donors. II. Samples used, extract prep, and labeling 1. Biosource: Human donor globes from NDRI (63, 71, 74 years old) and ARPE-19 cells. 2. Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (plastic, Matrigel, collagen I, collagen IV, laminin, and fibronectin). 3. Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturer’s instructions. 4. Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP. 5. No external controls were added. III. Hybridization procedures and parameters 1. Sample, array type, batch and serial # used 2. Hybridization protocol: Hybridization was carried out using the manufacturer’s recommendations. Arrays were prehybridized with Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS. IV. Measurement data and specifications of data processing 1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis. 3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis. Keywords: other
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Project description:Nkx2-5-GFP+ cells were collected by FACS from whole embryos (E8.0-8.5, 5-12 ps) and dissected heart tubes (E9.0-9.5, 15-21 ps). Because limited numbers of cells were obtained from individual embryos (~300 cells at E8, ~1500 cells at E9.5) mRNA was amplified twice with T7 RNA polymerase and fluorescent cDNA targets were synthesized by the indirect method with either Cy5 or Cy3. Targets from individual Nkx2-5 heterozygous and homozygous null cells were co-hybridized with cDNA probes printed on glass slide microarrays. Two microarray clone sets were used for each hybridization: the NIA/NIH 15,000 clone set derived from mouse non-cardiac embryonic tissue, and a ~6000 cardiac clone set derived in house.
2006-11-27 | E-MEXP-533 | biostudies-arrayexpress
Project description:Description I. Exp Design 1. Type of experiment: Comparison of native versus cultured RPE cells 2. Experimental factors: Native RPE versus ARPE-19 cells grown in different culture conditions 3. How many hybridizations in exp: 20 4. If a common reference used for all the hybs: no 5. Quality control steps: three independent arrays for each condition, and five different donor globes for native RPE 6. Description: The expression profile of ARPE-19 cells grown under different culture conditions were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 5 donors. II. Samples used, extract prep, and labeling 1. Biosource: Human donor globes from NDRI and Sierra Eye and Tissue Bank, and ARPE-19 cells. 2. Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (subconfluent culture density in presence of serum, confluent culture density in presence of serum, confluent culture density with serum withdrawn medium, differentiated (grown for 2.5 months) in serum, and differentiated (grown for 2.5 months) and then serum withdrawn medium). 3. Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturer's instructions. 4. Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP. 5. No external controls were added. III. Hybridization procedures and parameters 1. Sample, array type, batch and serial # used 2. Hybridization protocol: Hybridization was carried out using the manufacturer's recommendations. Arrays were prehybridized with Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS. IV. Measurement data and specifications of data processing 1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis. 3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis. Keywords: other
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Project description:I. Exp Design 1. Type of experiment: Comparison of native versus cultured RPE cells 2. Experimental factors: Native RPE versus ARPE-19 cells grown on different matrices 3. How many hybridizations in exp: 21 4. If a common reference used for all the hybs: no 5. Quality control steps: three independent arrays for each condition 6. Description: The expression profile of ARPE-19 cells grown on different matrices were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 3 donors. II. Samples used, extract prep, and labeling 1. Biosource: Human donor globes from NDRI (63, 71, 74 years old) and ARPE-19 cells. 2. Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (plastic, Matrigel, collagen I, collagen IV, laminin, and fibronectin). 3. Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturerâs instructions. 4. Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP. 5. No external controls were added. III. Hybridization procedures and parameters 1. Sample, array type, batch and serial # used 2. Hybridization protocol: Hybridization was carried out using the manufacturerâs recommendations. Arrays were prehybridized with Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS. IV. Measurement data and specifications of data processing 1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis. 3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis.
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Project description:Description I. Exp Design 1. Type of experiment: Comparison of native versus cultured RPE cells 2. Experimental factors: Native RPE versus ARPE-19 cells grown in different culture conditions 3. How many hybridizations in exp: 20 4. If a common reference used for all the hybs: no 5. Quality control steps: three independent arrays for each condition, and five different donor globes for native RPE 6. Description: The expression profile of ARPE-19 cells grown under different culture conditions were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 5 donors. II. Samples used, extract prep, and labeling 1. Biosource: Human donor globes from NDRI and Sierra Eye and Tissue Bank, and ARPE-19 cells. 2. Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (subconfluent culture density in presence of serum, confluent culture density in presence of serum, confluent culture density with serum withdrawn medium, differentiated (grown for 2.5 months) in serum, and differentiated (grown for 2.5 months) and then serum withdrawn medium). 3. Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturer's instructions. 4. Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP. 5. No external controls were added. III. Hybridization procedures and parameters 1. Sample, array type, batch and serial # used 2. Hybridization protocol: Hybridization was carried out using the manufacturer's recommendations. Arrays were prehybridized with Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS. IV. Measurement data and specifications of data processing 1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis. 3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis.
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