Search results for the GEO ID: GSE10806  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM272753 | GPL1261 |
|
Embryonic Stem cells sample 1
|
Embryonic Stem cells (OG2/Rosa26)
|
embryonic stem cells; strain: OG2/Rosa26
|
Washing and staining of the arrays was done in an Affymetrix GeneChip Fluidics station 450. The following default Affymetrix washing/staining protocol with antibody amplification was used:
(1) 10 cycles with 6xSSPE/0.01%Tween at 25˚C
(2) 4 cycles with 100 mM MES/ 0.1 M[Na+]/0.01% Tween at 50˚C
(3) 10 min. staining with 10 mg/mL Streptavidin/Phycoerythrin (SAPE, Molecular Probes) and 2 mg/mL acetylated BSA (GIBCO) in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(4) as (1)
(5) 10 min. staining with 3 mg/mL biotinylated anti-strepavidin antibody (goat, Vector Laboratories), 0.1 mg/mL goat IgG (Sigma), 2 mg/mL acetylated BSA in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(6) as (3)
(7) 15 cycles with 6xSSPE/0.01%Tween at 30˚C
|
| Sample_geo_accession | GSM272753
| | Sample_status | Public on Jun 28 2008
| | Sample_submission_date | Mar 12 2008
| | Sample_last_update_date | May 04 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | Embryonic Stem cells (ESC) 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 maufacturer'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 ml 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 mg of labeled cRNA in 200 ml 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 scan 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/GSM272nnn/GSM272753/suppl/GSM272753.CEL.gz
| | Sample_series_id | GSE10806
| | Sample_data_row_count | 45101
| | |
|
GSM272836 | GPL1261 |
|
Embryonic Stem cells sample 2
|
Embryonic Stem cells (OG2/Rosa26)
|
embryonic stem cells; strain: OG2/Rosa26
|
Washing and staining of the arrays was done in an Affymetrix GeneChip Fluidics station 450. The following default Affymetrix washing/staining protocol with antibody amplification was used:
(1) 10 cycles with 6xSSPE/0.01%Tween at 25˚C
(2) 4 cycles with 100 mM MES/ 0.1 M[Na+]/0.01% Tween at 50˚C
(3) 10 min. staining with 10 mg/mL Streptavidin/Phycoerythrin (SAPE, Molecular Probes) and 2 mg/mL acetylated BSA (GIBCO) in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(4) as (1)
(5) 10 min. staining with 3 mg/mL biotinylated anti-strepavidin antibody (goat, Vector Laboratories), 0.1 mg/mL goat IgG (Sigma), 2 mg/mL acetylated BSA in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(6) as (3)
(7) 15 cycles with 6xSSPE/0.01%Tween at 30˚C
|
| Sample_geo_accession | GSM272836
| | Sample_status | Public on Jun 28 2008
| | Sample_submission_date | Mar 12 2008
| | Sample_last_update_date | May 04 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | Embryonic Stem cells (ESC) 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 maufacturer'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 ml 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 mg of labeled cRNA in 200 ml 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 scan 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/GSM272nnn/GSM272836/suppl/GSM272836.CEL.gz
| | Sample_series_id | GSE10806
| | Sample_data_row_count | 45101
| | |
|
GSM272837 | GPL1261 |
|
Embryonic Stem cells sample 3
|
Embryonic Stem cells (OG2/Rosa26)
|
embryonic stem cells; strain: OG2/Rosa26
|
Washing and staining of the arrays was done in an Affymetrix GeneChip Fluidics station 450. The following default Affymetrix washing/staining protocol with antibody amplification was used:
(1) 10 cycles with 6xSSPE/0.01%Tween at 25˚C
(2) 4 cycles with 100 mM MES/ 0.1 M[Na+]/0.01% Tween at 50˚C
(3) 10 min. staining with 10 mg/mL Streptavidin/Phycoerythrin (SAPE, Molecular Probes) and 2 mg/mL acetylated BSA (GIBCO) in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(4) as (1)
(5) 10 min. staining with 3 mg/mL biotinylated anti-strepavidin antibody (goat, Vector Laboratories), 0.1 mg/mL goat IgG (Sigma), 2 mg/mL acetylated BSA in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(6) as (3)
(7) 15 cycles with 6xSSPE/0.01%Tween at 30˚C
|
| Sample_geo_accession | GSM272837
| | Sample_status | Public on Jun 28 2008
| | Sample_submission_date | Mar 12 2008
| | Sample_last_update_date | May 04 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | Embryonic Stem cells (ESC) 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 maufacturer'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 ml 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 mg of labeled cRNA in 200 ml 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 scan 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/GSM272nnn/GSM272837/suppl/GSM272837.CEL.gz
| | Sample_series_id | GSE10806
| | Sample_data_row_count | 45101
| | |
|
GSM272839 | GPL1261 |
|
Induced pluripotent stem (iPS) cells (Oct4, Klf4) sample 2
|
iPS cells 2 factors
|
induced pluripotent stem (ips) cells from mouse neural stem cells (nsc). strain: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
Washing and staining of the arrays was done in an Affymetrix GeneChip Fluidics station 450. The following default Affymetrix washing/staining protocol with antibody amplification was used:
(1) 10 cycles with 6xSSPE/0.01%Tween at 25˚C
(2) 4 cycles with 100 mM MES/ 0.1 M[Na+]/0.01% Tween at 50˚C
(3) 10 min. staining with 10 mg/mL Streptavidin/Phycoerythrin (SAPE, Molecular Probes) and 2 mg/mL acetylated BSA (GIBCO) in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(4) as (1)
(5) 10 min. staining with 3 mg/mL biotinylated anti-strepavidin antibody (goat, Vector Laboratories), 0.1 mg/mL goat IgG (Sigma), 2 mg/mL acetylated BSA in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(6) as (3)
(7) 15 cycles with 6xSSPE/0.01%Tween at 30˚C
|
| Sample_geo_accession | GSM272839
| | Sample_status | Public on Jun 28 2008
| | Sample_submission_date | Mar 12 2008
| | Sample_last_update_date | May 04 2011
| | 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 postnatal brain (day 5) 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 vectors encoding mouse cDNA of Oct4, Klf4 (1:1). Two days after infection, cells were further subcultured on irradiated MEF 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 maufacturer'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 ml 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 mg of labeled cRNA in 200 ml 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 scan 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/GSM272nnn/GSM272839/suppl/GSM272839.CEL.gz
| | Sample_series_id | GSE10806
| | Sample_data_row_count | 45101
| | |
|
GSM272846 | GPL1261 |
|
Induced pluripotent stem (iPS) cells (Oct4, Klf4) sample 3
|
iPS cells 2 factors
|
induced pluripotent stem (ips) cells from mouse neural stem cells (nsc). strain: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
Washing and staining of the arrays was done in an Affymetrix GeneChip Fluidics station 450. The following default Affymetrix washing/staining protocol with antibody amplification was used:
(1) 10 cycles with 6xSSPE/0.01%Tween at 25˚C
(2) 4 cycles with 100 mM MES/ 0.1 M[Na+]/0.01% Tween at 50˚C
(3) 10 min. staining with 10 mg/mL Streptavidin/Phycoerythrin (SAPE, Molecular Probes) and 2 mg/mL acetylated BSA (GIBCO) in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(4) as (1)
(5) 10 min. staining with 3 mg/mL biotinylated anti-strepavidin antibody (goat, Vector Laboratories), 0.1 mg/mL goat IgG (Sigma), 2 mg/mL acetylated BSA in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(6) as (3)
(7) 15 cycles with 6xSSPE/0.01%Tween at 30˚C
|
| Sample_geo_accession | GSM272846
| | Sample_status | Public on Jun 28 2008
| | Sample_submission_date | Mar 12 2008
| | Sample_last_update_date | May 04 2011
| | 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 postnatal brain (day 5) 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 vectors encoding mouse cDNA of Oct4, Klf4 (1:1). Two days after infection, cells were further subcultured on irradiated MEF 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 maufacturer'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 ml 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 mg of labeled cRNA in 200 ml 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 scan 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/GSM272nnn/GSM272846/suppl/GSM272846.CEL.gz
| | Sample_series_id | GSE10806
| | Sample_data_row_count | 45101
| | |
|
GSM272847 | GPL1261 |
|
Neural stem cells (NSC) 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
|
Washing and staining of the arrays was done in an Affymetrix GeneChip Fluidics station 450. The following default Affymetrix washing/staining protocol with antibody amplification was used:
(1) 10 cycles with 6xSSPE/0.01%Tween at 25˚C
(2) 4 cycles with 100 mM MES/ 0.1 M[Na+]/0.01% Tween at 50˚C
(3) 10 min. staining with 10 mg/mL Streptavidin/Phycoerythrin (SAPE, Molecular Probes) and 2 mg/mL acetylated BSA (GIBCO) in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(4) as (1)
(5) 10 min. staining with 3 mg/mL biotinylated anti-strepavidin antibody (goat, Vector Laboratories), 0.1 mg/mL goat IgG (Sigma), 2 mg/mL acetylated BSA in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(6) as (3)
(7) 15 cycles with 6xSSPE/0.01%Tween at 30˚C
|
| Sample_geo_accession | GSM272847
| | Sample_status | Public on Jun 28 2008
| | Sample_submission_date | Mar 12 2008
| | Sample_last_update_date | May 04 2011
| | 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 postnatal brain (day 5) 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 (NSC) were derived from postnatal brain (day 5) 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 maufacturer'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 ml 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 mg of labeled cRNA in 200 ml 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 scan 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/GSM272nnn/GSM272847/suppl/GSM272847.CEL.gz
| | Sample_series_id | GSE10806
| | Sample_data_row_count | 45101
| | |
|
GSM272848 | GPL1261 |
|
Neural Stem cells (NSC) 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.
|
Washing and staining of the arrays was done in an Affymetrix GeneChip Fluidics station 450. The following default Affymetrix washing/staining protocol with antibody amplification was used:
(1) 10 cycles with 6xSSPE/0.01%Tween at 25˚C
(2) 4 cycles with 100 mM MES/ 0.1 M[Na+]/0.01% Tween at 50˚C
(3) 10 min. staining with 10 mg/mL Streptavidin/Phycoerythrin (SAPE, Molecular Probes) and 2 mg/mL acetylated BSA (GIBCO) in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(4) as (1)
(5) 10 min. staining with 3 mg/mL biotinylated anti-strepavidin antibody (goat, Vector Laboratories), 0.1 mg/mL goat IgG (Sigma), 2 mg/mL acetylated BSA in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(6) as (3)
(7) 15 cycles with 6xSSPE/0.01%Tween at 30˚C
|
| Sample_geo_accession | GSM272848
| | Sample_status | Public on Jun 28 2008
| | Sample_submission_date | Mar 12 2008
| | Sample_last_update_date | May 04 2011
| | 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 postnatal brain (day 5) 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 (NSC) were derived from postnatal brain (day 5) 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 maufacturer'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 ml 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 mg of labeled cRNA in 200 ml 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 scan 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/GSM272nnn/GSM272848/suppl/GSM272848.CEL.gz
| | Sample_series_id | GSE10806
| | Sample_data_row_count | 45101
| | |
|
GSM272890 | GPL1261 |
|
Induced pluripotent stem (iPS) cells (Oct4, Klf4) sample 1
|
iPS cells 2 factors
|
induced pluripotent stem (ips) cells from mouse neural stem cells (nsc). strain: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
Washing and staining of the arrays was done in an Affymetrix GeneChip Fluidics station 450. The following default Affymetrix washing/staining protocol with antibody amplification was used:
(1) 10 cycles with 6xSSPE/0.01%Tween at 25˚C
(2) 4 cycles with 100 mM MES/ 0.1 M[Na+]/0.01% Tween at 50˚C
(3) 10 min. staining with 10 mg/mL Streptavidin/Phycoerythrin (SAPE, Molecular Probes) and 2 mg/mL acetylated BSA (GIBCO) in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(4) as (1)
(5) 10 min. staining with 3 mg/mL biotinylated anti-strepavidin antibody (goat, Vector Laboratories), 0.1 mg/mL goat IgG (Sigma), 2 mg/mL acetylated BSA in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(6) as (3)
(7) 15 cycles with 6xSSPE/0.01%Tween at 30˚C
|
| Sample_geo_accession | GSM272890
| | Sample_status | Public on Jun 28 2008
| | Sample_submission_date | Mar 13 2008
| | Sample_last_update_date | May 04 2011
| | 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 postnatal brain (day 5) 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 vectors encoding mouse cDNA of Oct4, Klf4 (1:1). Two days after infection, cells were further subcultured on irradiated MEF 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 maufacturer'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 ml 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 mg of labeled cRNA in 200 ml 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 scan 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/GSM272nnn/GSM272890/suppl/GSM272890.CEL.gz
| | Sample_series_id | GSE10806
| | Sample_data_row_count | 45101
| | |
|
GSM279200 | GPL1261 |
|
Induced pluripotent stem (iPS) cells (Oct4, Sox2, c-Myc, Klf4) sample 1
|
iPS cells 4 factors
|
induced pluripotent stem (ips) cells from mouse neural stem cells (nsc). strain: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
Washing and staining of the arrays was done in an Affymetrix GeneChip Fluidics station 450. The following default Affymetrix washing/staining protocol with antibody amplification was used:
(1) 10 cycles with 6xSSPE/0.01%Tween at 25˚C
(2) 4 cycles with 100 mM MES/ 0.1 M[Na+]/0.01% Tween at 50˚C
(3) 10 min. staining with 10 mg/mL Streptavidin/Phycoerythrin (SAPE, Molecular Probes) and 2 mg/mL acetylated BSA (GIBCO) in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(4) as (1)
(5) 10 min. staining with 3 mg/mL biotinylated anti-strepavidin antibody (goat, Vector Laboratories), 0.1 mg/mL goat IgG (Sigma), 2 mg/mL acetylated BSA in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(6) as (3)
(7) 15 cycles with 6xSSPE/0.01%Tween at 30˚C
|
| Sample_geo_accession | GSM279200
| | Sample_status | Public on Jun 28 2008
| | Sample_submission_date | Apr 04 2008
| | Sample_last_update_date | May 04 2011
| | 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 postnatal brain (day 5) 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 vectors encoding mouse cDNA of Oct4, Sox2, c-Myc, Klf4 (1:1:1:1). Two days after infection, cells were further subcultured on irradiated MEF 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 maufacturer'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 ml 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 mg of labeled cRNA in 200 ml 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 scan 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/GSM279nnn/GSM279200/suppl/GSM279200.CEL.gz
| | Sample_series_id | GSE10806
| | Sample_data_row_count | 45101
| | |
|
GSM279201 | GPL1261 |
|
Induced pluripotent stem (iPS) cells (Oct4, Sox2, c-Myc, Klf4) sample 2
|
iPS cells 4 factors
|
induced pluripotent stem (ips) cells from mouse neural stem cells (nsc). strain: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
Washing and staining of the arrays was done in an Affymetrix GeneChip Fluidics station 450. The following default Affymetrix washing/staining protocol with antibody amplification was used:
(1) 10 cycles with 6xSSPE/0.01%Tween at 25˚C
(2) 4 cycles with 100 mM MES/ 0.1 M[Na+]/0.01% Tween at 50˚C
(3) 10 min. staining with 10 mg/mL Streptavidin/Phycoerythrin (SAPE, Molecular Probes) and 2 mg/mL acetylated BSA (GIBCO) in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(4) as (1)
(5) 10 min. staining with 3 mg/mL biotinylated anti-strepavidin antibody (goat, Vector Laboratories), 0.1 mg/mL goat IgG (Sigma), 2 mg/mL acetylated BSA in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(6) as (3)
(7) 15 cycles with 6xSSPE/0.01%Tween at 30˚C
|
| Sample_geo_accession | GSM279201
| | Sample_status | Public on Jun 28 2008
| | Sample_submission_date | Apr 04 2008
| | Sample_last_update_date | May 04 2011
| | 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 postnatal brain (day 5) 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 vectors encoding mouse cDNA of Oct4, Sox2, c-Myc, Klf4 (1:1:1:1). Two days after infection, cells were further subcultured on irradiated MEF 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 maufacturer'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 ml 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 mg of labeled cRNA in 200 ml 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 scan 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/GSM279nnn/GSM279201/suppl/GSM279201.CEL.gz
| | Sample_series_id | GSE10806
| | Sample_data_row_count | 45101
| | |
|
GSM279202 | GPL1261 |
|
Induced pluripotent stem (iPS) cells (Oct4, Sox2, c-Myc, Klf4) sample 3
|
iPS cells 4 factors
|
induced pluripotent stem (ips) cells from mouse neural stem cells (nsc). strain: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.
|
Washing and staining of the arrays was done in an Affymetrix GeneChip Fluidics station 450. The following default Affymetrix washing/staining protocol with antibody amplification was used:
(1) 10 cycles with 6xSSPE/0.01%Tween at 25˚C
(2) 4 cycles with 100 mM MES/ 0.1 M[Na+]/0.01% Tween at 50˚C
(3) 10 min. staining with 10 mg/mL Streptavidin/Phycoerythrin (SAPE, Molecular Probes) and 2 mg/mL acetylated BSA (GIBCO) in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(4) as (1)
(5) 10 min. staining with 3 mg/mL biotinylated anti-strepavidin antibody (goat, Vector Laboratories), 0.1 mg/mL goat IgG (Sigma), 2 mg/mL acetylated BSA in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(6) as (3)
(7) 15 cycles with 6xSSPE/0.01%Tween at 30˚C
|
| Sample_geo_accession | GSM279202
| | Sample_status | Public on Jun 28 2008
| | Sample_submission_date | Apr 04 2008
| | Sample_last_update_date | May 04 2011
| | 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 postnatal brain (day 5) 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 vectors encoding mouse cDNA of Oct4, Sox2, c-Myc, Klf4 (1:1:1:1). Two days after infection, cells were further subcultured on irradiated MEF 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 maufacturer'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 ml 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 mg of labeled cRNA in 200 ml 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 scan 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/GSM279nnn/GSM279202/suppl/GSM279202.CEL.gz
| | Sample_series_id | GSE10806
| | Sample_data_row_count | 45101
| | |
|
| |
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