Search results for the GEO ID: GSE12499  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM314038 | GPL1261 |
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NSCs-derived iPS cells by one-factor (Oct4) sample_1
|
One-factor (1F) iPS cells
|
Induced pluripotent stem (iPS) cells from mouse neural stem cells (NSCs). Strain: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM314038
| | Sample_status | Public on Feb 01 2009
| | Sample_submission_date | Aug 20 2008
| | Sample_last_update_date | Oct 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Neural stem cells (NSC) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate and infected with pMX-based retroviral vector encoding mouse cDNA of Oct4. Three days after infection cells were further subcultured in ESC medium containing LIF without any further selection. Oct4-GFP–positive colonies were mechanically isolated, and individual cells were dissociated and subsequently replated onto MEF. Colonies were then selected for expansion.
| | Sample_growth_protocol_ch1 | Induced pluripotent stem (iPS) cell were grown on irradiated MEF and in ESC medium (DMEM supplemented with 15% FBS, nonessential amino acids, L-glutamine, penicillin/streptomycin, b-mercaptoethanol and 1,000 U/ml LIF).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314038/suppl/GSM314038.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314038/suppl/GSM314038.CHP.gz
| | Sample_series_id | GSE12499
| | Sample_data_row_count | 45101
| | |
|
GSM314039 | GPL1261 |
|
NSCs-derived iPS cells by one-factor (Oct4) sample_2
|
One-factor (1F) iPS cells
|
Induced pluripotent stem (iPS) cells from mouse neural stem cells (NSCs). Strain: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM314039
| | Sample_status | Public on Feb 01 2009
| | Sample_submission_date | Aug 20 2008
| | Sample_last_update_date | Oct 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Neural stem cells (NSC) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate and infected with pMX-based retroviral vector encoding mouse cDNA of Oct4. Three days after infection cells were further subcultured in ESC medium containing LIF without any further selection. Oct4-GFP–positive colonies were mechanically isolated, and individual cells were dissociated and subsequently replated onto MEF. Colonies were then selected for expansion.
| | Sample_growth_protocol_ch1 | Induced pluripotent stem (iPS) cell were grown on irradiated MEF and in ESC medium (DMEM supplemented with 15% FBS, nonessential amino acids, L-glutamine, penicillin/streptomycin, b-mercaptoethanol and 1,000 U/ml LIF).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314039/suppl/GSM314039.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314039/suppl/GSM314039.CHP.gz
| | Sample_series_id | GSE12499
| | Sample_data_row_count | 45101
| | |
|
GSM314040 | GPL1261 |
|
NSCs-derived iPS cells by one-factor (Oct4) sample_3
|
One-factor (1F) iPS cells
|
Induced pluripotent stem (iPS) cells from mouse neural stem cells (NSCs). Strain: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM314040
| | Sample_status | Public on Feb 01 2009
| | Sample_submission_date | Aug 20 2008
| | Sample_last_update_date | Oct 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Neural stem cells (NSC) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate and infected with pMX-based retroviral vector encoding mouse cDNA of Oct4. Three days after infection cells were further subcultured in ESC medium containing LIF without any further selection. Oct4-GFP–positive colonies were mechanically isolated, and individual cells were dissociated and subsequently replated onto MEF. Colonies were then selected for expansion.
| | Sample_growth_protocol_ch1 | Induced pluripotent stem (iPS) cell were grown on irradiated MEF and in ESC medium (DMEM supplemented with 15% FBS, nonessential amino acids, L-glutamine, penicillin/streptomycin, b-mercaptoethanol and 1,000 U/ml LIF).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314040/suppl/GSM314040.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314040/suppl/GSM314040.CHP.gz
| | Sample_series_id | GSE12499
| | Sample_data_row_count | 45101
| | |
|
GSM314042 | GPL1261 |
|
One-factor (Oct4) iPS cell-derived NSCs sample_1
|
NSCs from 1F (Oct4) iPS cells
|
Neural stem cells (NSCs) from one-factor (1F) iPS cells. Strain: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM314042
| | Sample_status | Public on Feb 01 2009
| | Sample_submission_date | Aug 20 2008
| | Sample_last_update_date | Oct 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate and infected with pMX-based retroviral vector encoding mouse cDNA of Oct4. Three days after infection cells were further subcultured in ESC medium containing LIF without any further selection to derived 1F (Oct4) iPS cells. These 1F iPS cells were differentiated into NSC according to Conti et al., (PLoS Biology, 2005) with modifications (Jeong Beom Kim, unpublished).
| | Sample_growth_protocol_ch1 | Neural stem cells (NSCs) were derived from 1F (Oct4) iPS cells of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004). Cells were seeded at a density of 5x104 cells per 6-well plate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314042/suppl/GSM314042.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314042/suppl/GSM314042.CHP.gz
| | Sample_series_id | GSE12499
| | Sample_data_row_count | 45101
| | |
|
GSM314043 | GPL1261 |
|
One-factor (Oct4) iPS cell-derived NSCs sample_2
|
NSCs from 1F (Oct4) iPS cells
|
Neural stem cells (NSCs) from one-factor (1F) iPS cells. Strain: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM314043
| | Sample_status | Public on Feb 01 2009
| | Sample_submission_date | Aug 20 2008
| | Sample_last_update_date | Oct 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate and infected with pMX-based retroviral vector encoding mouse cDNA of Oct4. Three days after infection cells were further subcultured in ESC medium containing LIF without any further selection to derived 1F (Oct4) iPS cells. These 1F iPS cells were differentiated into NSC according to Conti et al., (PLoS Biology, 2005) with modifications (Jeong Beom Kim, unpublished).
| | Sample_growth_protocol_ch1 | Neural stem cells (NSCs) were derived from 1F (Oct4) iPS cells of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004). Cells were seeded at a density of 5x104 cells per 6-well plate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314043/suppl/GSM314043.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314043/suppl/GSM314043.CHP.gz
| | Sample_series_id | GSE12499
| | Sample_data_row_count | 45101
| | |
|
GSM314044 | GPL1261 |
|
One-factor (Oct4) iPS cell-derived NSCs sample_3
|
NSCs from 1F (Oct4) iPS cells
|
Neural stem cells (NSCs) from one-factor (1F) iPS cells. Strain: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM314044
| | Sample_status | Public on Feb 01 2009
| | Sample_submission_date | Aug 20 2008
| | Sample_last_update_date | Oct 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate and infected with pMX-based retroviral vector encoding mouse cDNA of Oct4. Three days after infection cells were further subcultured in ESC medium containing LIF without any further selection to derived 1F (Oct4) iPS cells. These 1F iPS cells were differentiated into NSC according to Conti et al., (PLoS Biology, 2005) with modifications (Jeong Beom Kim, unpublished).
| | Sample_growth_protocol_ch1 | Neural stem cells (NSCs) were derived from 1F (Oct4) iPS cells of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004). Cells were seeded at a density of 5x104 cells per 6-well plate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314044/suppl/GSM314044.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314044/suppl/GSM314044.CHP.gz
| | Sample_series_id | GSE12499
| | Sample_data_row_count | 45101
| | |
|
GSM314045 | GPL1261 |
|
Neural stem cell sample_1
|
Neural stem cells (OG2/Rosa26)
|
Neural stem cells; Strain:OG2/Rosa26; Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM314045
| | Sample_status | Public on Feb 01 2009
| | Sample_submission_date | Aug 20 2008
| | Sample_last_update_date | Oct 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
| | Sample_growth_protocol_ch1 | Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314045/suppl/GSM314045.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314045/suppl/GSM314045.CHP.gz
| | Sample_series_id | GSE12499
| | Sample_data_row_count | 45101
| | |
|
GSM314046 | GPL1261 |
|
Neural stem cell sample_2
|
Neural stem cells (OG2/Rosa26)
|
Neural stem cells; Strain:OG2/Rosa26; Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM314046
| | Sample_status | Public on Feb 01 2009
| | Sample_submission_date | Aug 20 2008
| | Sample_last_update_date | Oct 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
| | Sample_growth_protocol_ch1 | Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314046/suppl/GSM314046.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314046/suppl/GSM314046.CHP.gz
| | Sample_series_id | GSE12499
| | Sample_data_row_count | 45101
| | |
|
GSM314047 | GPL1261 |
|
Neural stem cell sample_3
|
Neural stem cells (OG2/Rosa26)
|
Neural stem cells; Strain:OG2/Rosa26; Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM314047
| | Sample_status | Public on Feb 01 2009
| | Sample_submission_date | Aug 20 2008
| | Sample_last_update_date | Oct 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
| | Sample_growth_protocol_ch1 | Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314047/suppl/GSM314047.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314047/suppl/GSM314047.CHP.gz
| | Sample_series_id | GSE12499
| | Sample_data_row_count | 45101
| | |
|
GSM314048 | GPL1261 |
|
Neural stem cell sample_4
|
Neural stem cells (OG2/Rosa26)
|
Neural stem cells; Strain:OG2/Rosa26; Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM314048
| | Sample_status | Public on Feb 01 2009
| | Sample_submission_date | Aug 20 2008
| | Sample_last_update_date | Oct 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
| | Sample_growth_protocol_ch1 | Neural stem cells (NSCs) were derived from adult mouse brain of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females. Cells were seeded at a density of 5x104 cells per 6-well plate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314048/suppl/GSM314048.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM314nnn/GSM314048/suppl/GSM314048.CHP.gz
| | Sample_series_id | GSE12499
| | Sample_data_row_count | 45101
| | |
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