Search results for the GEO ID: GSE15944  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM399469 | GPL1355 |
|
Breast tumor biopsy_hydroxytyrosol_07SE120
|
Breast tumor biopsy, hydroxytyrosol, 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 before treatment with hydroxytyrosol. Such biopsy was taken when tumor had 2cm3 volume
biopsy dimensions: 0.7 cm x 2.5 mm
treatment: none
sample: 66D2 (basal)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399469
| | 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 protocol
| | 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/GSM399469/suppl/GSM399469.CEL.gz
| | Sample_series_id | GSE15944
| | Sample_data_row_count | 31099
| | |
|
GSM399474 | GPL1355 |
|
Total breast tumor_hydroxytyrosol_07SE135
|
Total breast tumor, hydroxytyrosol, 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: hydroxytyrosol (0,5 mg/kg weight/day, 5 days/week, for 6 weeks) by gavage after trucut biopsy.
sacrifice: 7th week post-biopsy
sample: 66D2 (final)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399474
| | 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 protocol
| | 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/GSM399474/suppl/GSM399474.CEL.gz
| | Sample_series_id | GSE15944
| | Sample_data_row_count | 31099
| | |
|
GSM399475 | GPL1355 |
|
Breast tumor biopsy_hydroxytyrosol_07SE121
|
Breast tumor biopsy, hydroxytyrosol, 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 before treatment with hydroxytyrosol. Such biopsy was taken when tumor had 2cm3 volume
biopsy dimensions: 0.7 cm x 2.5 mm
treatment: none
sample: 67D3(basal)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399475
| | 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 protocol
| | 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/GSM399475/suppl/GSM399475.CEL.gz
| | Sample_series_id | GSE15944
| | Sample_data_row_count | 31099
| | |
|
GSM399476 | GPL1355 |
|
Total breast tumor_hydroxytyrosol_07SE136
|
Total breast tumor, hydroxytyrosol, 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: hydroxytyrosol (0,5 mg/kg weight/day, 5 days/week, for 6 weeks) by gavage after trucut biopsy.
sacrifice: 7th week post-biopsy
sample: 67D3 (final)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399476
| | 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 protocol
| | 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/GSM399476/suppl/GSM399476.CEL.gz
| | Sample_series_id | GSE15944
| | Sample_data_row_count | 31099
| | |
|
GSM399477 | GPL1355 |
|
Breast tumor biopsy_hydroxytyrosol_07SE122
|
Breast tumor biopsy, hydroxytyrosol, 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 before treatment with hydroxytyrosol. Such biopsy was taken when tumor had 2cm3 volume
biopsy dimensions: 0.7 cm x 2.5 mm
treatment: none
sample: 45D3 (basal)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399477
| | 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 protocol
| | 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/GSM399477/suppl/GSM399477.CEL.gz
| | Sample_series_id | GSE15944
| | Sample_data_row_count | 31099
| | |
|
GSM399478 | GPL1355 |
|
Total breast tumor_hydroxytyrosol_07SE137
|
Total breast tumor, hydroxytyrosol, 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: hydroxytyrosol (0,5 mg/kg weight/day, 5 days/week, for 6 weeks) by gavage after trucut biopsy.
sacrifice: 7th week post-biopsy
sample: 45D3 (final)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399478
| | 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 protocol
| | 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/GSM399478/suppl/GSM399478.CEL.gz
| | Sample_series_id | GSE15944
| | Sample_data_row_count | 31099
| | |
|
GSM399892 | GPL1355 |
|
Breast tumor biopsy_hydroxytyrosol_07SE123
|
Breast tumor biopsy, hydroxytyrosol, 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 before treatment with hydroxytyrosol. Such biopsy was taken when tumor had 2cm3 volume
biopsy dimensions: 0.7 cm x 2.5 mm
treatment: none
sample: 49I1 (basal)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399892
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | May 04 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 protocol
| | 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/GSM399892/suppl/GSM399892.CEL.gz
| | Sample_series_id | GSE15944
| | Sample_data_row_count | 31099
| | |
|
GSM399893 | GPL1355 |
|
Total breast tumor_hydroxytyrosol_07SE138
|
Total breast tumor, hydroxytyrosol, 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: hydroxytyrosol (0,5 mg/kg weight/day, 5 days/week, for 6 weeks) by gavage after trucut biopsy.
sacrifice: 7th week post-biopsy
sample: 49I1 (final)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399893
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | May 04 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 protocol
| | 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/GSM399893/suppl/GSM399893.CEL.gz
| | Sample_series_id | GSE15944
| | Sample_data_row_count | 31099
| | |
|
GSM399894 | GPL1355 |
|
Breast tumor biopsy_hydroxytyrosol_07SE124
|
Breast tumor biopsy, hydroxytyrosol, 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 before treatment with hydroxytyrosol. Such biopsy was taken when tumor had 2cm3 volume
biopsy dimensions: 0.7 cm x 2.5 mm
treatment: none
sample: 51I1 (basal)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399894
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | May 04 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 protocol
| | 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/GSM399894/suppl/GSM399894.CEL.gz
| | Sample_series_id | GSE15944
| | Sample_data_row_count | 31099
| | |
|
GSM399912 | GPL1355 |
|
Total breast tumor_hydroxytyrosol_07SE139
|
Total breast tumor, hydroxytyrosol, 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: hydroxytyrosol (0,5 mg/kg weight/day, 5 days/week, for 6 weeks) by gavage after trucut biopsy.
sacrifice: 7th week post-biopsy
sample: 51I1 (final)
|
Affymetrix standard protocols
|
| Sample_geo_accession | GSM399912
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | May 04 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 protocol
| | 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/GSM399912/suppl/GSM399912.CEL.gz
| | Sample_series_id | GSE15944
| | Sample_data_row_count | 31099
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