Search results for the GEO ID: GSE27391  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM677358 | GPL1261 |
|
Spot14+ rep1
|
Spot14+ rep1
|
cell type: neural stem cell
spot14 gfp status: Spot14 GFP positive
|
replicate 1
|
| Sample_geo_accession | GSM677358
| | Sample_status | Public on Nov 02 2012
| | Sample_submission_date | Feb 17 2011
| | Sample_last_update_date | Nov 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin XS Kit (Macherey&Nagel)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Fragmentation and biotin labelling was done with the NuGEN Encore Biotin Module (NuGEN Inc.)
| | Sample_hyb_protocol | The amplification and array hybridisation were performed by Biolytix AG Switzerland as followed according to the manufacturer's procedures: the OvationTM RNA amplification SystemV2 (NuGEN Inc.) was used to generate cDNA followed by a cleanup step using Agencourt Beads RNA clean (Agnecourt Beckman Coulter Genomics). Hybridization, washing and staining were performed according to the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip Expression 3' Amplification Reagent Hybridization Controls and the Hybridization Module of GeneChip Hybridization Wash and Stain Kit and mixed with amplified cDNA samples. GeneChip Arrays Mouse Genome 430 2.0 were treated according manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip Fluidics Station 450 and scanning with GeneChip Scanner 3000 (Affymetrix).
| | Sample_scan_protocol | Data generation was controlled by the Affymetrix GeneChip Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix).
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA (Wu et al. Journal of American Statistical Association 99(468) 909-917 2004). Scatter plots were performed using in-house developed functions in Matlab.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Marcos,J,Araúzo-Bravo
| | Sample_contact_email | mararabra@yahoo.co.uk
| | Sample_contact_phone | +49 251 70365 326
| | Sample_contact_laboratory | Computational Biology and Bioinformatics
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | Max Planck Institute for Molecular Biomedicine
| | Sample_contact_address | Rontgenstr. 20
| | Sample_contact_city | Muenster
| | Sample_contact_zip/postal_code | 48149
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://www.mpi-muenster.mpg.de/ncd/arauzoe.shtml
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM677nnn/GSM677358/suppl/GSM677358.CEL.gz
| | Sample_series_id | GSE27391
| | Sample_data_row_count | 45101
| | |
|
GSM677359 | GPL1261 |
|
Spot14+ rep2
|
Spot14+ rep2
|
cell type: neural stem cell
spot14 gfp status: Spot14 GFP positive
|
replicate 2
|
| Sample_geo_accession | GSM677359
| | Sample_status | Public on Nov 02 2012
| | Sample_submission_date | Feb 17 2011
| | Sample_last_update_date | Nov 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin XS Kit (Macherey&Nagel)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Fragmentation and biotin labelling was done with the NuGEN Encore Biotin Module (NuGEN Inc.)
| | Sample_hyb_protocol | The amplification and array hybridisation were performed by Biolytix AG Switzerland as followed according to the manufacturer's procedures: the OvationTM RNA amplification SystemV2 (NuGEN Inc.) was used to generate cDNA followed by a cleanup step using Agencourt Beads RNA clean (Agnecourt Beckman Coulter Genomics). Hybridization, washing and staining were performed according to the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip Expression 3' Amplification Reagent Hybridization Controls and the Hybridization Module of GeneChip Hybridization Wash and Stain Kit and mixed with amplified cDNA samples. GeneChip Arrays Mouse Genome 430 2.0 were treated according manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip Fluidics Station 450 and scanning with GeneChip Scanner 3000 (Affymetrix).
| | Sample_scan_protocol | Data generation was controlled by the Affymetrix GeneChip Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix).
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA (Wu et al. Journal of American Statistical Association 99(468) 909-917 2004). Scatter plots were performed using in-house developed functions in Matlab.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Marcos,J,Araúzo-Bravo
| | Sample_contact_email | mararabra@yahoo.co.uk
| | Sample_contact_phone | +49 251 70365 326
| | Sample_contact_laboratory | Computational Biology and Bioinformatics
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | Max Planck Institute for Molecular Biomedicine
| | Sample_contact_address | Rontgenstr. 20
| | Sample_contact_city | Muenster
| | Sample_contact_zip/postal_code | 48149
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://www.mpi-muenster.mpg.de/ncd/arauzoe.shtml
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM677nnn/GSM677359/suppl/GSM677359.CEL.gz
| | Sample_series_id | GSE27391
| | Sample_data_row_count | 45101
| | |
|
GSM677360 | GPL1261 |
|
Spot14+ rep3
|
Spot14+ rep3
|
cell type: neural stem cell
spot14 gfp status: Spot14 GFP positive
|
replicate 3
|
| Sample_geo_accession | GSM677360
| | Sample_status | Public on Nov 02 2012
| | Sample_submission_date | Feb 17 2011
| | Sample_last_update_date | Nov 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin XS Kit (Macherey&Nagel)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Fragmentation and biotin labelling was done with the NuGEN Encore Biotin Module (NuGEN Inc.)
| | Sample_hyb_protocol | The amplification and array hybridisation were performed by Biolytix AG Switzerland as followed according to the manufacturer's procedures: the OvationTM RNA amplification SystemV2 (NuGEN Inc.) was used to generate cDNA followed by a cleanup step using Agencourt Beads RNA clean (Agnecourt Beckman Coulter Genomics). Hybridization, washing and staining were performed according to the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip Expression 3' Amplification Reagent Hybridization Controls and the Hybridization Module of GeneChip Hybridization Wash and Stain Kit and mixed with amplified cDNA samples. GeneChip Arrays Mouse Genome 430 2.0 were treated according manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip Fluidics Station 450 and scanning with GeneChip Scanner 3000 (Affymetrix).
| | Sample_scan_protocol | Data generation was controlled by the Affymetrix GeneChip Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix).
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA (Wu et al. Journal of American Statistical Association 99(468) 909-917 2004). Scatter plots were performed using in-house developed functions in Matlab.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Marcos,J,Araúzo-Bravo
| | Sample_contact_email | mararabra@yahoo.co.uk
| | Sample_contact_phone | +49 251 70365 326
| | Sample_contact_laboratory | Computational Biology and Bioinformatics
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | Max Planck Institute for Molecular Biomedicine
| | Sample_contact_address | Rontgenstr. 20
| | Sample_contact_city | Muenster
| | Sample_contact_zip/postal_code | 48149
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://www.mpi-muenster.mpg.de/ncd/arauzoe.shtml
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM677nnn/GSM677360/suppl/GSM677360.CEL.gz
| | Sample_series_id | GSE27391
| | Sample_data_row_count | 45101
| | |
|
GSM677361 | GPL1261 |
|
Spot14- rep1
|
Spot14- rep1
|
cell type: neural stem cell
spot14 gfp status: Spot14 GFP negative
|
replicate 1
|
| Sample_geo_accession | GSM677361
| | Sample_status | Public on Nov 02 2012
| | Sample_submission_date | Feb 17 2011
| | Sample_last_update_date | Nov 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin XS Kit (Macherey&Nagel)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Fragmentation and biotin labelling was done with the NuGEN Encore Biotin Module (NuGEN Inc.)
| | Sample_hyb_protocol | The amplification and array hybridisation were performed by Biolytix AG Switzerland as followed according to the manufacturer's procedures: the OvationTM RNA amplification SystemV2 (NuGEN Inc.) was used to generate cDNA followed by a cleanup step using Agencourt Beads RNA clean (Agnecourt Beckman Coulter Genomics). Hybridization, washing and staining were performed according to the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip Expression 3' Amplification Reagent Hybridization Controls and the Hybridization Module of GeneChip Hybridization Wash and Stain Kit and mixed with amplified cDNA samples. GeneChip Arrays Mouse Genome 430 2.0 were treated according manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip Fluidics Station 450 and scanning with GeneChip Scanner 3000 (Affymetrix).
| | Sample_scan_protocol | Data generation was controlled by the Affymetrix GeneChip Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix).
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA (Wu et al. Journal of American Statistical Association 99(468) 909-917 2004). Scatter plots were performed using in-house developed functions in Matlab.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Marcos,J,Araúzo-Bravo
| | Sample_contact_email | mararabra@yahoo.co.uk
| | Sample_contact_phone | +49 251 70365 326
| | Sample_contact_laboratory | Computational Biology and Bioinformatics
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | Max Planck Institute for Molecular Biomedicine
| | Sample_contact_address | Rontgenstr. 20
| | Sample_contact_city | Muenster
| | Sample_contact_zip/postal_code | 48149
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://www.mpi-muenster.mpg.de/ncd/arauzoe.shtml
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM677nnn/GSM677361/suppl/GSM677361.CEL.gz
| | Sample_series_id | GSE27391
| | Sample_data_row_count | 45101
| | |
|
GSM677362 | GPL1261 |
|
Spot14- rep2
|
Spot14- rep2
|
cell type: neural stem cell
spot14 gfp status: Spot14 GFP negative
|
replicate 2
|
| Sample_geo_accession | GSM677362
| | Sample_status | Public on Nov 02 2012
| | Sample_submission_date | Feb 17 2011
| | Sample_last_update_date | Nov 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin XS Kit (Macherey&Nagel)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Fragmentation and biotin labelling was done with the NuGEN Encore Biotin Module (NuGEN Inc.)
| | Sample_hyb_protocol | The amplification and array hybridisation were performed by Biolytix AG Switzerland as followed according to the manufacturer's procedures: the OvationTM RNA amplification SystemV2 (NuGEN Inc.) was used to generate cDNA followed by a cleanup step using Agencourt Beads RNA clean (Agnecourt Beckman Coulter Genomics). Hybridization, washing and staining were performed according to the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip Expression 3' Amplification Reagent Hybridization Controls and the Hybridization Module of GeneChip Hybridization Wash and Stain Kit and mixed with amplified cDNA samples. GeneChip Arrays Mouse Genome 430 2.0 were treated according manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip Fluidics Station 450 and scanning with GeneChip Scanner 3000 (Affymetrix).
| | Sample_scan_protocol | Data generation was controlled by the Affymetrix GeneChip Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix).
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA (Wu et al. Journal of American Statistical Association 99(468) 909-917 2004). Scatter plots were performed using in-house developed functions in Matlab.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Marcos,J,Araúzo-Bravo
| | Sample_contact_email | mararabra@yahoo.co.uk
| | Sample_contact_phone | +49 251 70365 326
| | Sample_contact_laboratory | Computational Biology and Bioinformatics
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | Max Planck Institute for Molecular Biomedicine
| | Sample_contact_address | Rontgenstr. 20
| | Sample_contact_city | Muenster
| | Sample_contact_zip/postal_code | 48149
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://www.mpi-muenster.mpg.de/ncd/arauzoe.shtml
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM677nnn/GSM677362/suppl/GSM677362.CEL.gz
| | Sample_series_id | GSE27391
| | Sample_data_row_count | 45101
| | |
|
GSM677363 | GPL1261 |
|
Spot14- rep3
|
Spot14- rep3
|
cell type: neural stem cell
spot14 gfp status: Spot14 GFP negative
|
replicate 3
|
| Sample_geo_accession | GSM677363
| | Sample_status | Public on Nov 02 2012
| | Sample_submission_date | Feb 17 2011
| | Sample_last_update_date | Nov 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin XS Kit (Macherey&Nagel)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Fragmentation and biotin labelling was done with the NuGEN Encore Biotin Module (NuGEN Inc.)
| | Sample_hyb_protocol | The amplification and array hybridisation were performed by Biolytix AG Switzerland as followed according to the manufacturer's procedures: the OvationTM RNA amplification SystemV2 (NuGEN Inc.) was used to generate cDNA followed by a cleanup step using Agencourt Beads RNA clean (Agnecourt Beckman Coulter Genomics). Hybridization, washing and staining were performed according to the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip Expression 3' Amplification Reagent Hybridization Controls and the Hybridization Module of GeneChip Hybridization Wash and Stain Kit and mixed with amplified cDNA samples. GeneChip Arrays Mouse Genome 430 2.0 were treated according manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip Fluidics Station 450 and scanning with GeneChip Scanner 3000 (Affymetrix).
| | Sample_scan_protocol | Data generation was controlled by the Affymetrix GeneChip Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix).
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA (Wu et al. Journal of American Statistical Association 99(468) 909-917 2004). Scatter plots were performed using in-house developed functions in Matlab.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Marcos,J,Araúzo-Bravo
| | Sample_contact_email | mararabra@yahoo.co.uk
| | Sample_contact_phone | +49 251 70365 326
| | Sample_contact_laboratory | Computational Biology and Bioinformatics
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | Max Planck Institute for Molecular Biomedicine
| | Sample_contact_address | Rontgenstr. 20
| | Sample_contact_city | Muenster
| | Sample_contact_zip/postal_code | 48149
| | Sample_contact_country | Germany
| | Sample_contact_web_link | http://www.mpi-muenster.mpg.de/ncd/arauzoe.shtml
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM677nnn/GSM677363/suppl/GSM677363.CEL.gz
| | Sample_series_id | GSE27391
| | Sample_data_row_count | 45101
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