Search results for the GEO ID: GSE16232  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM398893 | GPL1355 |
|
Breast tumor biopsy_DMBA_07SE115
|
Breast tumor biopsy, DMBA, basal moment
|
strain: Sprague-Dawley
gender: female
age: 12 weeks
tissue: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene. Such biopsy was taken when tumor had 2cm3 volume.
biopsy dimensions: 0.7 cm x 2.5 mm
treatment: none
sample: 31D3 (basal)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM398893
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Apr 29 2009
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a RNeasy Mini Kit from Qiagen, and later homogenized with QIAshredder (Quiagen) columns. Quality and quantity was assessed by agarose electrophoresis and spectrophotometric analysis (Absorbance 260/280 nm)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix's One-cycle target labeling (IVT Labeling kit from Affymetrix)
| | Sample_hyb_protocol | Affymetrix GeneChip Hybridization standard protocol
| | Sample_scan_protocol | Affymetrix GeneChip scan standard protocol
| | Sample_data_processing | Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v7.3.1 software (Agilent). Each trucut biopsy sample (basal moment) was normalized versus itself at the moment of the sacrifice (final moment) (Paired samples comparison). Compared data from experimental conditions are normalized versus array's base line mean considered for each case. This would be in the second line of the comparison (e.g. A vs B. Is normalized A and B respecting B). Thus, differentially expressed genes are presented as Fold Change values (Final vs Basal), for each breast tumor.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sergio,,Granados
| | Sample_contact_email | sergiogp@ugr.es
| | Sample_contact_institute | University of Granada
| | Sample_contact_address | Avenida del Conocimiento
| | Sample_contact_city | Granada
| | Sample_contact_zip/postal_code | 18071
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM398nnn/GSM398893/suppl/GSM398893.CEL.gz
| | Sample_series_id | GSE16232
| | Sample_data_row_count | 31099
| | |
|
GSM398894 | GPL1355 |
|
Total breast tumor_DMBA_07SE130
|
Total breast tumor, DMBA, final moment
|
strain: Sprague-Dawley
gender: female
age: 19 weeks
tissue: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice.
treatment: none
sample: 31D3 (final)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM398894
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Apr 29 2009
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a RNeasy Mini Kit from Qiagen, and later homogenized with QIAshredder (Quiagen) columns. Quality and quantity was assessed by agarose electrophoresis and spectrophotometric analysis (Absorbance 260/280 nm)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix's One-cycle target labeling (IVT Labeling kit from Affymetrix)
| | Sample_hyb_protocol | Affymetrix GeneChip Hybridization standard protocol
| | Sample_scan_protocol | Affymetrix GeneChip scan standard protocol
| | Sample_data_processing | Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v7.3.1 software (Agilent). Each trucut biopsy sample (basal moment) was normalized versus itself at the moment of the sacrifice (final moment) (Paired samples comparison). Compared data from experimental conditions are normalized versus array's base line mean considered for each case. This would be in the second line of the comparison (e.g. A vs B. Is normalized A and B respecting B). Thus, differentially expressed genes are presented as Fold Change values (Final vs Basal), for each breast tumor.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sergio,,Granados
| | Sample_contact_email | sergiogp@ugr.es
| | Sample_contact_institute | University of Granada
| | Sample_contact_address | Avenida del Conocimiento
| | Sample_contact_city | Granada
| | Sample_contact_zip/postal_code | 18071
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM398nnn/GSM398894/suppl/GSM398894.CEL.gz
| | Sample_series_id | GSE16232
| | Sample_data_row_count | 31099
| | |
|
GSM399028 | GPL1355 |
|
Breast tumor biopsy_DMBA_07SE116
|
Breast tumor biopsy, DMBA, basal moment
|
strain: Sprague-Dawley
gender: female
age: 12 weeks
tissue: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene. Such biopsy was taken when tumor had 2cm3 volume.
biopsy dimensions: 0.7 cm x 2.5 mm
treatment: none
sample: 32D1 (basal)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399028
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Apr 29 2009
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a RNeasy Mini Kit from Qiagen, and later homogenized with QIAshredder (Quiagen) columns. Quality and quantity was assessed by agarose electrophoresis and spectrophotometric analysis (Absorbance 260/280 nm)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix's One-cycle target labeling (IVT Labeling kit from Affymetrix)
| | Sample_hyb_protocol | Affymetrix GeneChip Hybridization standard protocol
| | Sample_scan_protocol | Affymetrix GeneChip scan standard protocol
| | Sample_data_processing | Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v7.3.1 software (Agilent). Each trucut biopsy sample (basal moment) was normalized versus itself at the moment of the sacrifice (final moment) (Paired samples comparison). Compared data from experimental conditions are normalized versus array's base line mean considered for each case. This would be in the second line of the comparison (e.g. A vs B. Is normalized A and B respecting B). Thus, differentially expressed genes are presented as Fold Change values (Final vs Basal), for each breast tumor.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sergio,,Granados
| | Sample_contact_email | sergiogp@ugr.es
| | Sample_contact_institute | University of Granada
| | Sample_contact_address | Avenida del Conocimiento
| | Sample_contact_city | Granada
| | Sample_contact_zip/postal_code | 18071
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399028/suppl/GSM399028.CEL.gz
| | Sample_series_id | GSE16232
| | Sample_data_row_count | 31099
| | |
|
GSM399030 | GPL1355 |
|
Total breast tumor_DMBA_07SE131
|
Total breast tumor, DMBA, final moment
|
strain: Sprague-Dawley
gender: female
age: 19 weeks
tissue: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice.
treatment: none
sample: 32D1 (final)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399030
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Apr 29 2009
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a RNeasy Mini Kit from Qiagen, and later homogenized with QIAshredder (Quiagen) columns. Quality and quantity was assessed by agarose electrophoresis and spectrophotometric analysis (Absorbance 260/280 nm)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix's One-cycle target labeling (IVT Labeling kit from Affymetrix)
| | Sample_hyb_protocol | Affymetrix GeneChip Hybridization standard protocol
| | Sample_scan_protocol | Affymetrix GeneChip scan standard protocol
| | Sample_data_processing | Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v7.3.1 software (Agilent). Each trucut biopsy sample (basal moment) was normalized versus itself at the moment of the sacrifice (final moment) (Paired samples comparison). Compared data from experimental conditions are normalized versus array's base line mean considered for each case. This would be in the second line of the comparison (e.g. A vs B. Is normalized A and B respecting B). Thus, differentially expressed genes are presented as Fold Change values (Final vs Basal), for each breast tumor.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sergio,,Granados
| | Sample_contact_email | sergiogp@ugr.es
| | Sample_contact_institute | University of Granada
| | Sample_contact_address | Avenida del Conocimiento
| | Sample_contact_city | Granada
| | Sample_contact_zip/postal_code | 18071
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399030/suppl/GSM399030.CEL.gz
| | Sample_series_id | GSE16232
| | Sample_data_row_count | 31099
| | |
|
GSM399430 | GPL1355 |
|
Breast tumor biopsy_DMBA_07SE117
|
Breast tumor biopsy, DMBA, basal moment
|
strain: Sprague-Dawley
gender: female
age: 12 weeks
tissue: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene. Such biopsy was taken when tumor had 2cm3 volume.
biopsy dimensions: 0.7 cm x 2.5 mm
treatment: none
sample: 37I1 (basal)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399430
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Apr 30 2009
| | Sample_last_update_date | Jan 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a RNeasy Mini Kit from Qiagen, and later homogenized with QIAshredder (Quiagen) columns. Quality and quantity was assessed by agarose electrophoresis and spectrophotometric analysis (Absorbance 260/280 nm)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix's One-cycle target labeling (IVT Labeling kit from Affymetrix)
| | Sample_hyb_protocol | Affymetrix GeneChip Hybridization standard protocol
| | Sample_scan_protocol | Affymetrix GeneChip scan standard protocol
| | Sample_data_processing | Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v7.3.1 software (Agilent). Each trucut biopsy sample (basal moment) was normalized versus itself at the moment of the sacrifice (final moment) (Paired samples comparison). Compared data from experimental conditions are normalized versus array's base line mean considered for each case. This would be in the second line of the comparison (e.g. A vs B. Is normalized A and B respecting B). Thus, differentially expressed genes are presented as Fold Change values (Final vs Basal), for each breast tumor.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sergio,,Granados
| | Sample_contact_email | sergiogp@ugr.es
| | Sample_contact_institute | University of Granada
| | Sample_contact_address | Avenida del Conocimiento
| | Sample_contact_city | Granada
| | Sample_contact_zip/postal_code | 18071
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399430/suppl/GSM399430.CEL.gz
| | Sample_series_id | GSE16232
| | Sample_data_row_count | 31099
| | |
|
GSM399433 | GPL1355 |
|
Total breast tumor_DMBA_07SE132
|
Total breast tumor, DMBA, final moment
|
strain: Sprague-Dawley
gender: female
age: 19 weeks
tissue: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice.
treatment: none
sample: 37I1 (final)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399433
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Apr 30 2009
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a RNeasy Mini Kit from Qiagen, and later homogenized with QIAshredder (Quiagen) columns. Quality and quantity was assessed by agarose electrophoresis and spectrophotometric analysis (Absorbance 260/280 nm)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix's One-cycle target labeling (IVT Labeling kit from Affymetrix)
| | Sample_hyb_protocol | Affymetrix GeneChip Hybridization standard protocol
| | Sample_scan_protocol | Affymetrix GeneChip scan standard protocol
| | Sample_data_processing | Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v7.3.1 software (Agilent). Each trucut biopsy sample (basal moment) was normalized versus itself at the moment of the sacrifice (final moment) (Paired samples comparison). Compared data from experimental conditions are normalized versus array's base line mean considered for each case. This would be in the second line of the comparison (e.g. A vs B. Is normalized A and B respecting B). Thus, differentially expressed genes are presented as Fold Change values (Final vs Basal), for each breast tumor.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sergio,,Granados
| | Sample_contact_email | sergiogp@ugr.es
| | Sample_contact_institute | University of Granada
| | Sample_contact_address | Avenida del Conocimiento
| | Sample_contact_city | Granada
| | Sample_contact_zip/postal_code | 18071
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399433/suppl/GSM399433.CEL.gz
| | Sample_series_id | GSE16232
| | Sample_data_row_count | 31099
| | |
|
GSM399434 | GPL1355 |
|
Breast tumor biopsy_DMBA_07SE118
|
Breast tumor biopsy, DMBA, basal moment
|
strain: Sprague-Dawley
gender: female
age: 12 weeks
tissue: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene. Such biopsy was taken when tumor had 2cm3 volume.
biopsy dimensions: 0.7 cm x 2.5 mm
treatment: none
sample: 50I1 (basal)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399434
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Apr 30 2009
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a RNeasy Mini Kit from Qiagen, and later homogenized with QIAshredder (Quiagen) columns. Quality and quantity was assessed by agarose electrophoresis and spectrophotometric analysis (Absorbance 260/280 nm)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix's One-cycle target labeling (IVT Labeling kit from Affymetrix)
| | Sample_hyb_protocol | Affymetrix GeneChip Hybridization standard protocol
| | Sample_scan_protocol | Affymetrix GeneChip scan standard protocol
| | Sample_data_processing | Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v7.3.1 software (Agilent). Each trucut biopsy sample (basal moment) was normalized versus itself at the moment of the sacrifice (final moment) (Paired samples comparison). Compared data from experimental conditions are normalized versus array's base line mean considered for each case. This would be in the second line of the comparison (e.g. A vs B. Is normalized A and B respecting B). Thus, differentially expressed genes are presented as Fold Change values (Final vs Basal), for each breast tumor.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sergio,,Granados
| | Sample_contact_email | sergiogp@ugr.es
| | Sample_contact_institute | University of Granada
| | Sample_contact_address | Avenida del Conocimiento
| | Sample_contact_city | Granada
| | Sample_contact_zip/postal_code | 18071
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399434/suppl/GSM399434.CEL.gz
| | Sample_series_id | GSE16232
| | Sample_data_row_count | 31099
| | |
|
GSM399456 | GPL1355 |
|
Total breast tumor_DMBA_07SE133
|
Total breast tumor, DMBA, final moment
|
strain: Sprague-Dawley
gender: female
age: 19 weeks
tissue: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice.
treatment: none
sample: 50I1 (final)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399456
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Apr 30 2009
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a RNeasy Mini Kit from Qiagen, and later homogenized with QIAshredder (Quiagen) columns. Quality and quantity was assessed by agarose electrophoresis and spectrophotometric analysis (Absorbance 260/280 nm)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix's One-cycle target labeling (IVT Labeling kit from Affymetrix)
| | Sample_hyb_protocol | Affymetrix GeneChip Hybridization standard protocol
| | Sample_scan_protocol | Affymetrix GeneChip scan standard protocol
| | Sample_data_processing | Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v7.3.1 software (Agilent). Each trucut biopsy sample (basal moment) was normalized versus itself at the moment of the sacrifice (final moment) (Paired samples comparison). Compared data from experimental conditions are normalized versus array's base line mean considered for each case. This would be in the second line of the comparison (e.g. A vs B. Is normalized A and B respecting B). Thus, differentially expressed genes are presented as Fold Change values (Final vs Basal), for each breast tumor.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sergio,,Granados
| | Sample_contact_email | sergiogp@ugr.es
| | Sample_contact_institute | University of Granada
| | Sample_contact_address | Avenida del Conocimiento
| | Sample_contact_city | Granada
| | Sample_contact_zip/postal_code | 18071
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399456/suppl/GSM399456.CEL.gz
| | Sample_series_id | GSE16232
| | Sample_data_row_count | 31099
| | |
|
GSM399460 | GPL1355 |
|
Breast tumor biopsy_DMBA_07SE119
|
Breast tumor biopsy, DMBA, basal moment
|
strain: Sprague-Dawley
gender: female
age: 12 weeks
tissue: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene. Such biopsy was taken when tumor had 2cm3 volume.
biopsy dimensions: 0.7 cm x 2.5 mm
treatment: none
sample: 52I4 (basal)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399460
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Apr 30 2009
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a RNeasy Mini Kit from Qiagen, and later homogenized with QIAshredder (Quiagen) columns. Quality and quantity was assessed by agarose electrophoresis and spectrophotometric analysis (Absorbance 260/280 nm)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix's One-cycle target labeling (IVT Labeling kit from Affymetrix)
| | Sample_hyb_protocol | Affymetrix GeneChip Hybridization standard protocol
| | Sample_scan_protocol | Affymetrix GeneChip scan standard protocol
| | Sample_data_processing | Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v7.3.1 software (Agilent). Each trucut biopsy sample (basal moment) was normalized versus itself at the moment of the sacrifice (final moment) (Paired samples comparison). Compared data from experimental conditions are normalized versus array's base line mean considered for each case. This would be in the second line of the comparison (e.g. A vs B. Is normalized A and B respecting B). Thus, differentially expressed genes are presented as Fold Change values (Final vs Basal), for each breast tumor.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sergio,,Granados
| | Sample_contact_email | sergiogp@ugr.es
| | Sample_contact_institute | University of Granada
| | Sample_contact_address | Avenida del Conocimiento
| | Sample_contact_city | Granada
| | Sample_contact_zip/postal_code | 18071
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399460/suppl/GSM399460.CEL.gz
| | Sample_series_id | GSE16232
| | Sample_data_row_count | 31099
| | |
|
GSM399466 | GPL1355 |
|
Total breast tumor_DMBA_07SE134
|
Total breast tumor, DMBA, final moment
|
strain: Sprague-Dawley
gender: female
age: 19 weeks
tissue: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice.
treatment: none
sample: 52I4(final)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399466
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Apr 30 2009
| | Sample_last_update_date | May 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a RNeasy Mini Kit from Qiagen, and later homogenized with QIAshredder (Quiagen) columns. Quality and quantity was assessed by agarose electrophoresis and spectrophotometric analysis (Absorbance 260/280 nm)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix's One-cycle target labeling (IVT Labeling kit from Affymetrix)
| | Sample_hyb_protocol | Affymetrix GeneChip Hybridization standard protocol
| | Sample_scan_protocol | Affymetrix GeneChip scan standard protocol
| | Sample_data_processing | Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v7.3.1 software (Agilent). Each trucut biopsy sample (basal moment) was normalized versus itself at the moment of the sacrifice (final moment) (Paired samples comparison). Compared data from experimental conditions are normalized versus array's base line mean considered for each case. This would be in the second line of the comparison (e.g. A vs B. Is normalized A and B respecting B). Thus, differentially expressed genes are presented as Fold Change values (Final vs Basal), for each breast tumor.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sergio,,Granados
| | Sample_contact_email | sergiogp@ugr.es
| | Sample_contact_institute | University of Granada
| | Sample_contact_address | Avenida del Conocimiento
| | Sample_contact_city | Granada
| | Sample_contact_zip/postal_code | 18071
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399466/suppl/GSM399466.CEL.gz
| | Sample_series_id | GSE16232
| | Sample_data_row_count | 31099
| | |
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