Search results for the GEO ID: GSE13718  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM344844 | GPL1261 |
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wild type 12.5 day murine embryo fibroblasts
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wild type murine embryo fibroblasts
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Murine embryos from wild type littermates were minced at 12.5 day and fibroblast cell lines established.
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Effect of depletion of EBp1 in knock out murine embryo fibroblasts.
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| Sample_geo_accession | GSM344844
| | Sample_status | Public on Mar 31 2009
| | Sample_submission_date | Nov 24 2008
| | Sample_last_update_date | Mar 31 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Zhang and Hamburger
| | Sample_treatment_protocol_ch1 | Embryos (12.5 days) were minced and incubated in 0.25% trypsin and 5 U of DNAse I for 37º C for 30 min. Dulbeccos MEM supplemented with 10% fetal bovine serum and penicillin and streptomycin were added to the cell suspension and cells centrifuged at 1000 rpm for 10 min.
| | Sample_growth_protocol_ch1 | Cells propagated in complete medium and 10% FBS. Passage 2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with Trizol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis and labeling. First and second strand cDNA were synthesized g of total RNA using the SuperScript Double-Stranded cDNA Synthesisfrom 5-15 Kit (Gibco Life Technologies) and oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) primer according to the manufacturer’s instructions.
| | Sample_label_protocol_ch1 | cRNA was synthesized labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter coupled double stranded cDNA as template and the T7 RNA Transcript Labeling Kit (ENZO Diagnostics Inc.). Briefly, double stranded cDNA synthesized from the previous steps were washed twice with 70% l Rnase-free H2O. The cDNA was incubated with 4ethanol and resuspended in 22 l of 10X each Reaction Buffer, Biotin Labeled Ribonucleotides, DTT, Rnase l 20X T7 RNA Polymerase for 5 hr at 37oC. The labeled cRNAInhibitor Mix and 2 was separated from unincorporated ribonucleotides by passing through a CHROMA SPIN-100 column (Clontech) and precipitated at –20oC for 1 hr to overnight
| | Sample_hyb_protocol | The cRNA pellet was resuspended and fragmented by heat and ion-mediated hydrolysis at 95oC for 35 mins in 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc. The fragmented cRNA was hybridized for 16hr at 45oC to U133A oligonucleotide arrays (Affymetrix) containing ~39,000 full length annotated genes together with additional probe sets designed to represent EST sequences. Arrays were washed at 25oC with 6 X SSPE (0.9M NaCl, 60 mMNaH2PO4, 6 mM EDTA + 0.01% Tween 20) followed by a stringent wash at 50oC with 100 mM MES, 0.1M [Na+], 0.01% Tween 20. The arrays were then stained with phycoerythrein conjugated streptavidin (Molecular Probes) and the fluorescence intensities were determined using a laser confocal scanner (Hewlett-Packard).
| | Sample_scan_protocol | The scanned images were analyzed using Microarray software (Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to constant target intensity (2500) for all arrays used
| | Sample_data_processing | Data Analysis was conducted using Microarray Suite 5.0 (Affymetrix) following user guidelines. The signal intensity for each gene was calculated as (PM - MM)/(number of probe“the average intensity difference, represented by [ pairs)], where PM and MM denote perfect-match and mismatch probes
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Anne,,Hamburger
| | Sample_contact_email | ahamburg@som.umaryland.edu
| | Sample_contact_department | Cancer Center
| | Sample_contact_institute | University of Maryland Baltimore
| | Sample_contact_address | 655 W. Baltimore St
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21201
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344844/suppl/GSM344844.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344844/suppl/GSM344844.CHP.gz
| | Sample_series_id | GSE13718
| | Sample_data_row_count | 45101
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GSM344846 | GPL1261 |
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Gene expression in Ebp1 knock out murine embryo fibroblasts
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Ebp1 knock out murine embryo (12.5 day) fibroblasts
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Murine embryos 12.5 day (Ebp1 knock out) were harvested and minced in trypsin. Fibroblasts were propagated as described.
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Expression of RNA in 12.5 day murine embryo fibroblasts from Ebp1 knock out mice.
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| Sample_geo_accession | GSM344846
| | Sample_status | Public on Mar 31 2009
| | Sample_submission_date | Nov 24 2008
| | Sample_last_update_date | Mar 31 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Zhang and Hamburger
| | Sample_treatment_protocol_ch1 | Embryos (12.5 days) were minced and incubated in 0.25% trypsin and 5 U of DNAse I for 37º C for 30 min. Dulbeccos MEM supplemented with 10% fetal bovine serum and penicillin and streptomycin were added to the cell suspension and cells centrifuged at 1000 rpm for 10 min.
| | Sample_growth_protocol_ch1 | Fibroblasts were propagated in complete media with 10% FBS. RNA harvested at passage 2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with Trizol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis and labeling. First and second strand cDNA were synthesized g of total RNA using the SuperScript Double-Stranded cDNA Synthesisfrom 5-15 Kit (Gibco Life Technologies) and oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) primer according to the manufacturer’s instructions.
| | Sample_label_protocol_ch1 | cRNA was synthesized labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter coupled double stranded cDNA as template and the T7 RNA Transcript Labeling Kit (ENZO Diagnostics Inc.). Briefly, double stranded cDNA synthesized from the previous steps were washed twice with 70% l Rnase-free H2O. The cDNA was incubated with 4ethanol and resuspended in 22 l of 10X each Reaction Buffer, Biotin Labeled Ribonucleotides, DTT, Rnase l 20X T7 RNA Polymerase for 5 hr at 37oC. The labeled cRNAInhibitor Mix and 2 was separated from unincorporated ribonucleotides by passing through a CHROMA SPIN-100 column (Clontech) and precipitated at –20oC for 1 hr to overnight
| | Sample_hyb_protocol | The cRNA pellet was resuspended and fragmented by heat and ion-mediated hydrolysis at 95oC for 35 mins in 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc. The fragmented cRNA was hybridized for 16hr at 45oC to U133A oligonucleotide arrays (Affymetrix) containing ~39,000 full length annotated genes together with additional probe sets designed to represent EST sequences. Arrays were washed at 25oC with 6 X SSPE (0.9M NaCl, 60 mMNaH2PO4, 6 mM EDTA + 0.01% Tween 20) followed by a stringent wash at 50oC with 100 mM MES, 0.1M [Na+], 0.01% Tween 20. The arrays were then stained with phycoerythrein conjugated streptavidin (Molecular Probes) and the fluorescence intensities were determined using a laser confocal scanner (Hewlett-Packard).
| | Sample_scan_protocol | The scanned images were analyzed using Microarray software (Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to constant target intensity (2500) for all arrays used.
| | Sample_data_processing | Data Analysis was conducted using Microarray Suite 5.0 (Affymetrix) following user guidelines. The signal intensity for each gene was calculated as (PM - MM)/(number of probe“the average intensity difference, represented by [ pairs)], where PM and MM denote perfect-match and mismatch probes
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Anne,,Hamburger
| | Sample_contact_email | ahamburg@som.umaryland.edu
| | Sample_contact_department | Cancer Center
| | Sample_contact_institute | University of Maryland Baltimore
| | Sample_contact_address | 655 W. Baltimore St
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21201
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344846/suppl/GSM344846.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM344nnn/GSM344846/suppl/GSM344846.CHP.gz
| | Sample_series_id | GSE13718
| | Sample_data_row_count | 45101
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