Home   Search   Browse   Statistics   User guide   FAQs   Post question   Download   Process data  
Search results for the GEO ID: GSE7647
(Click on the check boxes provided under "Select for analysis", to initiate grouping)
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)
GSM ID
GPL ID
Select for analysis
Title
Source name
Description
Characteristics
GSM184943
GPL339
Exp-1 Total RNA from mock L929 cells (5h) Total RNA from mock treated L929 murine fibroblast cells Total RNA from mock treated L929 murine fibroblast cells L929 cells were mock treated or infected at an MOI of 5 with either wildtype or nt3A mutant null-VRP, and total RNA was isolated at 5 hpi using the UltraSpec reagent protocol as described above. The UNC-CH Functional Genomics Core Facility provided Affymetrix sample preparation and hybridization services, hybridizing the samples to Affymetrix Mouse Expression 430A (MOE430A) GeneChip arrays, which include analysis of ~22,600 genes. cDNA was synthesized using 7 ug of total RNA and a custom cDNA kit from Life Technologies using a T7-(dT)24 primer for the reaction. Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit, and the cRNA was fragmented in fragmentation buffer (40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) at 94oC for 35 min. 15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD, and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween 20). 10 ug of cRNA was used for hybridization. The arrays were hybridized for 16 h at 45oC in the GeneChip Hybridization Oven 640, followed by washing and staining with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400. The arrays were then scanned with the Hewlett Packard GeneArray Scanner. Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis, with sample quality assessed by examination of 3’ to 5’ intensity ratios of certain genes. Expression analysis files created by Microarray Suite were imported into GeneSpring 6.2 (Silicon Genetics) for further gene expression analysis and filtering. Two independent array studies were completed, and gene lists were compiled representing only those genes that were up- or downregulated by greater than 2-fold in replicate analyses.
GSM184995
GPL339
Exp-1 Total RNA from wildtype VRP infected L929 cells (5h) Total RNA from wildtype null-VRP infected L929 murine fibroblast cells at 5hpi Total RNA isolated from murine L929 cells infected with wildtype null-VRP (Venezuelan equine encephalitis virus replicon particles) at 5 hrs post-infection. L929 cells were mock treated or infected at an MOI of 5 with either wildtype or nt3A mutant null-VRP, and total RNA was isolated at 5 hpi using the UltraSpec reagent protocol as described above. The UNC-CH Functional Genomics Core Facility provided Affymetrix sample preparation and hybridization services, hybridizing the samples to Affymetrix Mouse Expression 430A (MOE430A) GeneChip arrays, which include analysis of ~22,600 genes. cDNA was synthesized using 7 ug of total RNA and a custom cDNA kit from Life Technologies using a T7-(dT)24 primer for the reaction. Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit, and the cRNA was fragmented in fragmentation buffer (40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) at 94oC for 35 min. 15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD, and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween 20). 10 ug of cRNA was used for hybridization. The arrays were hybridized for 16 h at 45oC in the GeneChip Hybridization Oven 640, followed by washing and staining with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400. The arrays were then scanned with the Hewlett Packard GeneArray Scanner. Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis, with sample quality assessed by examination of 3’ to 5’ intensity ratios of certain genes. Expression analysis files created by Microarray Suite were imported into GeneSpring 6.2 (Silicon Genetics) for further gene expression analysis and filtering. Two independent array studies were completed, and gene lists were compiled representing only those genes that were up- or downregulated by greater than 2-fold in replicate analyses.
GSM184998
GPL339
Exp-1 Total RNA from nt3A mutant VRP infected L929 cells (5h) Total RNA from nt3A mutant null-VRP infected L929 murine fibroblast cells at 5hpi Total RNA isolated at 5 hrs post-infection from murine L929 cells infected with null-VRP (Venezuelan equine encephalitis virus replicon particles) containing the nt3A mutation. L929 cells were mock treated or infected at an MOI of 5 with either wildtype or nt3A mutant null-VRP, and total RNA was isolated at 5 hpi using the UltraSpec reagent protocol as described above. The UNC-CH Functional Genomics Core Facility provided Affymetrix sample preparation and hybridization services, hybridizing the samples to Affymetrix Mouse Expression 430A (MOE430A) GeneChip arrays, which include analysis of ~22,600 genes. cDNA was synthesized using 7 ug of total RNA and a custom cDNA kit from Life Technologies using a T7-(dT)24 primer for the reaction. Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit, and the cRNA was fragmented in fragmentation buffer (40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) at 94oC for 35 min. 15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD, and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween 20). 10 ug of cRNA was used for hybridization. The arrays were hybridized for 16 h at 45oC in the GeneChip Hybridization Oven 640, followed by washing and staining with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400. The arrays were then scanned with the Hewlett Packard GeneArray Scanner. Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis, with sample quality assessed by examination of 3’ to 5’ intensity ratios of certain genes. Expression analysis files created by Microarray Suite were imported into GeneSpring 6.2 (Silicon Genetics) for further gene expression analysis and filtering. Two independent array studies were completed, and gene lists were compiled representing only those genes that were up- or downregulated by greater than 2-fold in replicate analyses.
GSM185001
GPL339
Exp-2 Total RNA from mock L929 cells (5h) Total RNA from mock treated L929 murine fibroblast cells Total RNA from mock treated L929 murine fibroblast cells L929 cells were mock treated or infected at an MOI of 5 with either wildtype or nt3A mutant null-VRP, and total RNA was isolated at 5 hpi using the UltraSpec reagent protocol as described above. The UNC-CH Functional Genomics Core Facility provided Affymetrix sample preparation and hybridization services, hybridizing the samples to Affymetrix Mouse Expression 430A (MOE430A) GeneChip arrays, which include analysis of ~22,600 genes. cDNA was synthesized using 7 ug of total RNA and a custom cDNA kit from Life Technologies using a T7-(dT)24 primer for the reaction. Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit, and the cRNA was fragmented in fragmentation buffer (40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) at 94oC for 35 min. 15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD, and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween 20). 10 ug of cRNA was used for hybridization. The arrays were hybridized for 16 h at 45oC in the GeneChip Hybridization Oven 640, followed by washing and staining with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400. The arrays were then scanned with the Hewlett Packard GeneArray Scanner. Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis, with sample quality assessed by examination of 3’ to 5’ intensity ratios of certain genes. Expression analysis files created by Microarray Suite were imported into GeneSpring 6.2 (Silicon Genetics) for further gene expression analysis and filtering. Two independent array studies were completed, and gene lists were compiled representing only those genes that were up- or downregulated by greater than 2-fold in replicate analyses.
GSM185004
GPL339
Exp-2 Total RNA from wildtype VRP infected L929 cells (5h) Total RNA from wildtype null-VRP infected L929 murine fibroblast cells at 5hpi Total RNA isolated from murine L929 cells infected with wildtype null-VRP (Venezuelan equine encephalitis virus replicon particles) at 5 hrs post-infection. L929 cells were mock treated or infected at an MOI of 5 with either wildtype or nt3A mutant null-VRP, and total RNA was isolated at 5 hpi using the UltraSpec reagent protocol as described above. The UNC-CH Functional Genomics Core Facility provided Affymetrix sample preparation and hybridization services, hybridizing the samples to Affymetrix Mouse Expression 430A (MOE430A) GeneChip arrays, which include analysis of ~22,600 genes. cDNA was synthesized using 7 ug of total RNA and a custom cDNA kit from Life Technologies using a T7-(dT)24 primer for the reaction. Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit, and the cRNA was fragmented in fragmentation buffer (40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) at 94oC for 35 min. 15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD, and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween 20). 10 ug of cRNA was used for hybridization. The arrays were hybridized for 16 h at 45oC in the GeneChip Hybridization Oven 640, followed by washing and staining with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400. The arrays were then scanned with the Hewlett Packard GeneArray Scanner. Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis, with sample quality assessed by examination of 3’ to 5’ intensity ratios of certain genes. Expression analysis files created by Microarray Suite were imported into GeneSpring 6.2 (Silicon Genetics) for further gene expression analysis and filtering. Two independent array studies were completed, and gene lists were compiled representing only those genes that were up- or downregulated by greater than 2-fold in replicate analyses.
GSM185008
GPL339
Exp-2 Total RNA from nt3A mutant VRP infected L929 cells (5h) Total RNA from nt3A mutant null-VRP infected L929 murine fibroblast cells at 5hpi Total RNA isolated at 5 hrs post-infection from murine L929 cells infected with null-VRP (Venezuelan equine encephalitis virus replicon particles) containing the nt3A mutation. L929 cells were mock treated or infected at an MOI of 5 with either wildtype or nt3A mutant null-VRP, and total RNA was isolated at 5 hpi using the UltraSpec reagent protocol as described above. The UNC-CH Functional Genomics Core Facility provided Affymetrix sample preparation and hybridization services, hybridizing the samples to Affymetrix Mouse Expression 430A (MOE430A) GeneChip arrays, which include analysis of ~22,600 genes. cDNA was synthesized using 7 ug of total RNA and a custom cDNA kit from Life Technologies using a T7-(dT)24 primer for the reaction. Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit, and the cRNA was fragmented in fragmentation buffer (40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) at 94oC for 35 min. 15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD, and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween 20). 10 ug of cRNA was used for hybridization. The arrays were hybridized for 16 h at 45oC in the GeneChip Hybridization Oven 640, followed by washing and staining with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400. The arrays were then scanned with the Hewlett Packard GeneArray Scanner. Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis, with sample quality assessed by examination of 3’ to 5’ intensity ratios of certain genes. Expression analysis files created by Microarray Suite were imported into GeneSpring 6.2 (Silicon Genetics) for further gene expression analysis and filtering. Two independent array studies were completed, and gene lists were compiled representing only those genes that were up- or downregulated by greater than 2-fold in replicate analyses.
 
 
Make groups for comparisons
(2 groups will be compared at a time)
Select GSMs and click on "Add groups"
Enter the group name here:


Select expression type
Transcripts profile based on;
A. Differential status (Up/Down regulation)
B. Absolute calls (Transcribed/Not-detected)
 
Filter results by number of probes