Search results for the GEO ID: GSE6246 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM143330 | GPL339 |
|
NOR LAK sample III: NMRI mouse on the first day of lactation
|
mammary gland
|
Strain: NMRI, female, mammary gland on the first day of lactation
|
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
|
Sample_geo_accession | GSM143330
| Sample_status | Public on Mar 10 2007
| Sample_submission_date | Nov 01 2006
| Sample_last_update_date | Mar 09 2007
| 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 isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
| Sample_hyb_protocol | The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
| Sample_scan_protocol | Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
| Sample_data_processing | The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
| Sample_platform_id | GPL339
| Sample_contact_name | Andreas,,Klein
| Sample_contact_email | andreas.klein@charite.de
| Sample_contact_phone | +49 30 450 528087
| Sample_contact_fax | +49 30 450 52945
| Sample_contact_department | Institute of Biochemistry
| Sample_contact_institute | Charité (CCO)
| Sample_contact_address | Charitéplatz 1
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_contact_web_link | http://www.charite.de/molbiol/bioinf/tumbiol/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143330/suppl/GSM143330.CEL.gz
| Sample_series_id | GSE6246
| Sample_data_row_count | 22690
| |
|
GSM143697 | GPL339 |
|
NOR LAK sample I: NMRI mouse on the first day of lactation
|
mammary gland
|
Strain: NMRI, female, mammary gland on the first day of lactation
|
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
|
Sample_geo_accession | GSM143697
| Sample_status | Public on Mar 10 2007
| Sample_submission_date | Nov 07 2006
| Sample_last_update_date | Mar 09 2007
| 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 isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
| Sample_hyb_protocol | The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
| Sample_scan_protocol | Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
| Sample_data_processing | The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
| Sample_platform_id | GPL339
| Sample_contact_name | Andreas,,Klein
| Sample_contact_email | andreas.klein@charite.de
| Sample_contact_phone | +49 30 450 528087
| Sample_contact_fax | +49 30 450 52945
| Sample_contact_department | Institute of Biochemistry
| Sample_contact_institute | Charité (CCO)
| Sample_contact_address | Charitéplatz 1
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_contact_web_link | http://www.charite.de/molbiol/bioinf/tumbiol/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143697/suppl/GSM143697.CEL.gz
| Sample_series_id | GSE6246
| Sample_data_row_count | 22690
| |
|
GSM143891 | GPL339 |
|
NOR LAK sample II: NMRI mouse on the first day of lactation
|
mammary gland
|
Strain: NMRI, female, mammary gland on the first day of lactation
|
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
|
Sample_geo_accession | GSM143891
| Sample_status | Public on Mar 10 2007
| Sample_submission_date | Nov 08 2006
| Sample_last_update_date | Mar 09 2007
| 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 isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
| Sample_hyb_protocol | The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
| Sample_scan_protocol | Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
| Sample_data_processing | The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
| Sample_platform_id | GPL339
| Sample_contact_name | Andreas,,Klein
| Sample_contact_email | andreas.klein@charite.de
| Sample_contact_phone | +49 30 450 528087
| Sample_contact_fax | +49 30 450 52945
| Sample_contact_department | Institute of Biochemistry
| Sample_contact_institute | Charité (CCO)
| Sample_contact_address | Charitéplatz 1
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_contact_web_link | http://www.charite.de/molbiol/bioinf/tumbiol/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143891/suppl/GSM143891.CEL.gz
| Sample_series_id | GSE6246
| Sample_data_row_count | 22690
| |
|
GSM143903 | GPL339 |
|
WAP-SVT/t-LAK sample I: WAP-SVT/t mouse on the first day of lactation
|
mammary gland
|
This animal synthesizes the SV40 T/t- antigens selectively in the mammary gland epithelial cells. Strain: NMRI, female, mammary gland on the first day of lactation.
|
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
|
Sample_geo_accession | GSM143903
| Sample_status | Public on Mar 10 2007
| Sample_submission_date | Nov 08 2006
| Sample_last_update_date | Mar 09 2007
| 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 isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
| Sample_hyb_protocol | The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
| Sample_scan_protocol | Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
| Sample_data_processing | The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
| Sample_platform_id | GPL339
| Sample_contact_name | Andreas,,Klein
| Sample_contact_email | andreas.klein@charite.de
| Sample_contact_phone | +49 30 450 528087
| Sample_contact_fax | +49 30 450 52945
| Sample_contact_department | Institute of Biochemistry
| Sample_contact_institute | Charité (CCO)
| Sample_contact_address | Charitéplatz 1
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_contact_web_link | http://www.charite.de/molbiol/bioinf/tumbiol/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143903/suppl/GSM143903.CEL.gz
| Sample_series_id | GSE6246
| Sample_data_row_count | 22690
| |
|
GSM143904 | GPL339 |
|
WAP-SVT/t-LAK sample II: WAP-SVT/t mouse on the first day of lactation
|
mammary gland
|
This animal synthesizes the SV40 T/t- antigens selectively in the mammary gland epithelial cells. Strain: NMRI, female, mammary gland on the first day of lactation.
|
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
|
Sample_geo_accession | GSM143904
| Sample_status | Public on Mar 10 2007
| Sample_submission_date | Nov 08 2006
| Sample_last_update_date | Mar 09 2007
| 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 isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
| Sample_hyb_protocol | The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
| Sample_scan_protocol | Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
| Sample_data_processing | The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
| Sample_platform_id | GPL339
| Sample_contact_name | Andreas,,Klein
| Sample_contact_email | andreas.klein@charite.de
| Sample_contact_phone | +49 30 450 528087
| Sample_contact_fax | +49 30 450 52945
| Sample_contact_department | Institute of Biochemistry
| Sample_contact_institute | Charité (CCO)
| Sample_contact_address | Charitéplatz 1
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_contact_web_link | http://www.charite.de/molbiol/bioinf/tumbiol/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143904/suppl/GSM143904.CEL.gz
| Sample_series_id | GSE6246
| Sample_data_row_count | 22690
| |
|
GSM143906 | GPL339 |
|
WAP-SVT/t-LAK sample III: WAP-SVT/t mouse on the first day of lactation
|
mammary gland
|
This animal synthesizes the SV40 T/t- antigens selectively in the mammary gland epithelial cells. Strain: NMRI, female, mammary gland on the first day of lactation.
|
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
|
Sample_geo_accession | GSM143906
| Sample_status | Public on Mar 10 2007
| Sample_submission_date | Nov 08 2006
| Sample_last_update_date | Mar 09 2007
| 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 isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
| Sample_hyb_protocol | The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
| Sample_scan_protocol | Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
| Sample_data_processing | The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
| Sample_platform_id | GPL339
| Sample_contact_name | Andreas,,Klein
| Sample_contact_email | andreas.klein@charite.de
| Sample_contact_phone | +49 30 450 528087
| Sample_contact_fax | +49 30 450 52945
| Sample_contact_department | Institute of Biochemistry
| Sample_contact_institute | Charité (CCO)
| Sample_contact_address | Charitéplatz 1
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_contact_web_link | http://www.charite.de/molbiol/bioinf/tumbiol/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143906/suppl/GSM143906.CEL.gz
| Sample_series_id | GSE6246
| Sample_data_row_count | 22690
| |
|
GSM143908 | GPL339 |
|
583 tumor 1: WAP-SVT/t breast cancer
|
breast cancer
|
This animal synthesizes the SV40 T/t- antigens selectively in the mammary gland epithelial cells. Strain: NMRI, female, breast cancer.
|
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
|
Sample_geo_accession | GSM143908
| Sample_status | Public on Mar 10 2007
| Sample_submission_date | Nov 08 2006
| Sample_last_update_date | Mar 09 2007
| 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 isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
| Sample_hyb_protocol | The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
| Sample_scan_protocol | Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
| Sample_data_processing | The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
| Sample_platform_id | GPL339
| Sample_contact_name | Andreas,,Klein
| Sample_contact_email | andreas.klein@charite.de
| Sample_contact_phone | +49 30 450 528087
| Sample_contact_fax | +49 30 450 52945
| Sample_contact_department | Institute of Biochemistry
| Sample_contact_institute | Charité (CCO)
| Sample_contact_address | Charitéplatz 1
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_contact_web_link | http://www.charite.de/molbiol/bioinf/tumbiol/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143908/suppl/GSM143908.CEL.gz
| Sample_series_id | GSE6246
| Sample_data_row_count | 22690
| |
|
GSM143909 | GPL339 |
|
585pos1 tumor 2: WAP-SVT/t breast cancer
|
breast cancer
|
This animal synthesizes the SV40 T/t- antigens selectively in the mammary gland epithelial cells. Strain: NMRI, female, breast cancer.
|
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
|
Sample_geo_accession | GSM143909
| Sample_status | Public on Mar 10 2007
| Sample_submission_date | Nov 08 2006
| Sample_last_update_date | Mar 09 2007
| 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 isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
| Sample_hyb_protocol | The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
| Sample_scan_protocol | Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
| Sample_data_processing | The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
| Sample_platform_id | GPL339
| Sample_contact_name | Andreas,,Klein
| Sample_contact_email | andreas.klein@charite.de
| Sample_contact_phone | +49 30 450 528087
| Sample_contact_fax | +49 30 450 52945
| Sample_contact_department | Institute of Biochemistry
| Sample_contact_institute | Charité (CCO)
| Sample_contact_address | Charitéplatz 1
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_contact_web_link | http://www.charite.de/molbiol/bioinf/tumbiol/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143909/suppl/GSM143909.CEL.gz
| Sample_series_id | GSE6246
| Sample_data_row_count | 22690
| |
|
GSM143911 | GPL339 |
|
597pos7 tumor 3: WAP-SVT/t breast cancer
|
breast cancer
|
This animal synthesizes the SV40 T/t- antigens selectively in the mammary gland epithelial cells. Strain: NMRI, female, breast cancer.
|
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
|
Sample_geo_accession | GSM143911
| Sample_status | Public on Mar 10 2007
| Sample_submission_date | Nov 08 2006
| Sample_last_update_date | Mar 09 2007
| 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 isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
| Sample_hyb_protocol | The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
| Sample_scan_protocol | Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
| Sample_data_processing | The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
| Sample_platform_id | GPL339
| Sample_contact_name | Andreas,,Klein
| Sample_contact_email | andreas.klein@charite.de
| Sample_contact_phone | +49 30 450 528087
| Sample_contact_fax | +49 30 450 52945
| Sample_contact_department | Institute of Biochemistry
| Sample_contact_institute | Charité (CCO)
| Sample_contact_address | Charitéplatz 1
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_contact_web_link | http://www.charite.de/molbiol/bioinf/tumbiol/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143911/suppl/GSM143911.CEL.gz
| Sample_series_id | GSE6246
| Sample_data_row_count | 22690
| |
|
GSM143913 | GPL339 |
|
ME-A cells: breast cancer cell line
|
breast cancer cell line
|
Small tissue segments from the 583 tumor 1 were isolated and used to establish the ME-A cells. These cells show continuous T/t-antigen synthesis and are permanently T/t-antigen positive. They exhibit the morphology and growth characteristics of tumor cells.
|
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
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Sample_geo_accession | GSM143913
| Sample_status | Public on Nov 10 2006
| Sample_submission_date | Nov 08 2006
| Sample_last_update_date | Nov 09 2006
| 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 isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
| Sample_hyb_protocol | The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
| Sample_scan_protocol | Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
| Sample_data_processing | The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
| Sample_platform_id | GPL339
| Sample_contact_name | Andreas,,Klein
| Sample_contact_email | andreas.klein@charite.de
| Sample_contact_phone | +49 30 450 528087
| Sample_contact_fax | +49 30 450 52945
| Sample_contact_department | Institute of Biochemistry
| Sample_contact_institute | Charité (CCO)
| Sample_contact_address | Charitéplatz 1
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_contact_web_link | http://www.charite.de/molbiol/bioinf/tumbiol/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143913/suppl/GSM143913.CEL.gz
| Sample_series_id | GSE6246
| Sample_data_row_count | 22690
| |
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GSM143915 | GPL339 |
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Revertant ME-B cells: breast cancer cell line
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breast cancer cell line
|
Small tissue segments from the 583 tumor 1 were isolated and used to establish the revertant ME-B cells. These cells show (in contrast to the ME-A cells) a downregulation of the WAP-SVT/t gene expression. These cells, that were formerly of tumor origin regain the morphology and growth characteristic of non-tumor cells. This transition occurs mostly within the first days after plating under standard tissue culture conditions (DME-medium, 10% FCS).
|
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
|
Sample_geo_accession | GSM143915
| Sample_status | Public on Nov 10 2006
| Sample_submission_date | Nov 08 2006
| Sample_last_update_date | Nov 09 2006
| 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 isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
| Sample_hyb_protocol | The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
| Sample_scan_protocol | Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
| Sample_data_processing | The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
| Sample_platform_id | GPL339
| Sample_contact_name | Andreas,,Klein
| Sample_contact_email | andreas.klein@charite.de
| Sample_contact_phone | +49 30 450 528087
| Sample_contact_fax | +49 30 450 52945
| Sample_contact_department | Institute of Biochemistry
| Sample_contact_institute | Charité (CCO)
| Sample_contact_address | Charitéplatz 1
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_contact_web_link | http://www.charite.de/molbiol/bioinf/tumbiol/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143915/suppl/GSM143915.CEL.gz
| Sample_series_id | GSE6246
| Sample_data_row_count | 22690
| |
|
GSM143916 | GPL339 |
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Retransformed ME-B-T/t cells: breast cancer cell line
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breast cancer cell line
|
The revertant-ME-B cells were again reconverted into tumor cells by SV40 T/t. The pSVT/t DNA construct was transfected into revertant-ME-B cells and SV40 T/t-antigen positive cell clones were G418 selected. These clones were collected and designated as retransformed ME-B-T/t cells. The ME-B-T/t cells regained the morphology and growth characteristic of breast cancer cells.
|
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
|
Sample_geo_accession | GSM143916
| Sample_status | Public on Nov 10 2006
| Sample_submission_date | Nov 08 2006
| Sample_last_update_date | Nov 09 2006
| 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 isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
| Sample_hyb_protocol | The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
| Sample_scan_protocol | Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
| Sample_data_processing | The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
| Sample_platform_id | GPL339
| Sample_contact_name | Andreas,,Klein
| Sample_contact_email | andreas.klein@charite.de
| Sample_contact_phone | +49 30 450 528087
| Sample_contact_fax | +49 30 450 52945
| Sample_contact_department | Institute of Biochemistry
| Sample_contact_institute | Charité (CCO)
| Sample_contact_address | Charitéplatz 1
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_contact_web_link | http://www.charite.de/molbiol/bioinf/tumbiol/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143916/suppl/GSM143916.CEL.gz
| Sample_series_id | GSE6246
| Sample_data_row_count | 22690
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