Search results for the GEO ID: GSE28583  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM706202 | GPL570 |
|
Breast tumor biopsy_Prechemotherapy_08SE128
|
Breast tumor biopsy, Prechemotherapy
|
age: 39
gender: female
tissue: breast tumor
trucut biopsy: 3.5 cm x 1.75 mm
tumor biopsy acquisition: Such biopsy was taken at diagnosis
treatment: none (Prechemotherapy)
sample_id: 08SE128
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM706202
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 11 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM706nnn/GSM706202/suppl/GSM706202_08SE128HGU133Plus2.0_130608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM706687 | GPL570 |
|
Breast tumor biopsy_Prechemotherapy_08SE134
|
Breast tumor biopsy, Prechemotherapy
|
age: 70
gender: female
tissue: breast tumor
trucut biopsy: 3.5 cm x 1.75 mm
tumor biopsy acquisition: Such biopsy was taken at diagnosis
treatment: none (Prechemotherapy)
sample_id: 08SE134
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM706687
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 12 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM706nnn/GSM706687/suppl/GSM706687_08SE134HGU133Plus2.0_050608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM706689 | GPL570 |
|
Breast tumor biopsy_Prechemotherapy_08SE140
|
Breast tumor biopsy, Prechemotherapy
|
age: 58
gender: female
tissue: breast tumor
trucut biopsy: 3.5 cm x 1.75 mm
tumor biopsy acquisition: Such biopsy was taken at diagnosis
treatment: none (Prechemotherapy)
sample_id: 08SE140
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM706689
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 12 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM706nnn/GSM706689/suppl/GSM706689_08SE140HGU133Plus2.0_130608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM706692 | GPL570 |
|
Breast tumor biopsy_Prechemotherapy_08SE152
|
Breast tumor biopsy, Prechemotherapy
|
age: 69
gender: female
tissue: breast tumor
trucut biopsy: 3.5 cm x 1.75 mm
tumor biopsy acquisition: Such biopsy was taken at diagnosis
treatment: none (Prechemotherapy)
sample_id: 08SE152
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM706692
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 12 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM706nnn/GSM706692/suppl/GSM706692_08SE152HGU133Plus2.0_130608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM706699 | GPL570 |
|
Breast tumor biopsy_Prechemotherapy_08SE158
|
Breast tumor biopsy, Prechemotherapy
|
age: 42
gender: female
tissue: breast tumor
trucut biopsy: 3.5 cm x 1.75 mm
tumor biopsy acquisition: Such biopsy was taken at diagnosis
treatment: none (Prechemotherapy)
sample_id: 08SE158
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM706699
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 12 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM706nnn/GSM706699/suppl/GSM706699_08SE158HGU133Plus2.0_170608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM706703 | GPL570 |
|
Breast tumor biopsy_Prechemotherapy_08SE170
|
Breast tumor biopsy, Prechemotherapy
|
age: 55
gender: female
tissue: breast tumor
trucut biopsy: 3.5 cm x 1.75 mm
tumor biopsy acquisition: Such biopsy was taken at diagnosis
treatment: none (Prechemotherapy)
sample_id: 08SE170
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM706703
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 12 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM706nnn/GSM706703/suppl/GSM706703_08SE170HGU133Plus2.0_050608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM706705 | GPL570 |
|
Breast tumor biopsy_Prechemotherapy_08SE172
|
Breast tumor biopsy, Prechemotherapy
|
age: 48
gender: female
tissue: breast tumor
trucut biopsy: 3.5 cm x 1.75 mm
tumor biopsy acquisition: Such biopsy was taken at diagnosis
treatment: none (Prechemotherapy)
sample_id: 08SE172
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM706705
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 12 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM706nnn/GSM706705/suppl/GSM706705_08SE172HGU133Plus2.0_170608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM706710 | GPL570 |
|
Breast tumor biopsy_Prechemotherapy_08SE178
|
Breast tumor biopsy, Prechemotherapy
|
age: 58
gender: female
tissue: breast tumor
trucut biopsy: 3.5 cm x 1.75 mm
tumor biopsy acquisition: Such biopsy was taken at diagnosis
treatment: none (Prechemotherapy)
sample_id: 08SE178
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM706710
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 12 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM706nnn/GSM706710/suppl/GSM706710_08SE178HGU133Plus2.0_050608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM706711 | GPL570 |
|
Breast tumor biopsy_Prechemotherapy_08SE188
|
Breast tumor biopsy, Prechemotherapy
|
age: 53
gender: female
tissue: breast tumor
trucut biopsy: 3.5 cm x 1.75 mm
tumor biopsy acquisition: Such biopsy was taken at diagnosis
treatment: none (Prechemotherapy)
sample_id: 08SE188
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM706711
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 12 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM706nnn/GSM706711/suppl/GSM706711_08SE188HGU133Plus2.0_170608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM706712 | GPL570 |
|
Breast tumor biopsy_Prechemotherapy_08SE275
|
Breast tumor biopsy, Prechemotherapy
|
age: 53
gender: female
tissue: breast tumor
trucut biopsy: 3.5 cm x 1.75 mm
tumor biopsy acquisition: Such biopsy was taken at diagnosis
treatment: none (Prechemotherapy)
sample_id: 08SE275
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM706712
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 12 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM706nnn/GSM706712/suppl/GSM706712_08SE275HGU133Plus2.0_170608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM707554 | GPL570 |
|
Breast tumor biopsy_Postchemotherapy_08SE129
|
Breast tumor biopsy, Postchemotherapy
|
age: 39
gender: female
tissue: breast tumor
tumor biopsy acquisition: Such biopsy was taken from surgery specimen and selected by the pathologist in charge within 30 min. after tumor removal
treatment: C
sample_id: 08SE129
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM707554
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 13 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707554/suppl/GSM707554_08SE129HGU133Plus2.0_130608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM707555 | GPL570 |
|
Breast tumor biopsy_Postchemotherapy_08SE135
|
Breast tumor biopsy, Postchemotherapy
|
age: 70
gender: female
tissue: breast tumor
tumor biopsy acquisition: Such biopsy was taken from surgery specimen and selected by the pathologist in charge within 30 min. after tumor removal
treatment: A
sample_id: 08SE135
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM707555
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 13 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707555/suppl/GSM707555_08SE135HGU133Plus2.0_050608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM707556 | GPL570 |
|
Breast tumor biopsy_Postchemotherapy_08SE141
|
Breast tumor biopsy, Postchemotherapy
|
age: 58
gender: female
tissue: breast tumor
tumor biopsy acquisition: Such biopsy was taken from surgery specimen and selected by the pathologist in charge within 30 min. after tumor removal
treatment: A
sample_id: 08SE141
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM707556
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 13 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707556/suppl/GSM707556_08SE141HGU133Plus2.0_130608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM707560 | GPL570 |
|
Breast tumor biopsy_Postchemotherapy_08SE153
|
Breast tumor biopsy, Postchemotherapy
|
age: 69
gender: female
tissue: breast tumor
tumor biopsy acquisition: Such biopsy was taken from surgery specimen and selected by the pathologist in charge within 30 min. after tumor removal
treatment: C
sample_id: 08SE153
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM707560
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 13 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707560/suppl/GSM707560_08SE153HGU133Plus2.0_130608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM707561 | GPL570 |
|
Breast tumor biopsy_Postchemotherapy_08SE159
|
Breast tumor biopsy, Postchemotherapy
|
age: 42
gender: female
tissue: breast tumor
tumor biopsy acquisition: Such biopsy was taken from surgery specimen and selected by the pathologist in charge within 30 min. after tumor removal
treatment: C
sample_id: 08SE159
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM707561
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 13 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707561/suppl/GSM707561_08SE159HGU133Plus2.0_170608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM707580 | GPL570 |
|
Breast tumor biopsy_Postchemotherapy_08SE171
|
Breast tumor biopsy, Postchemotherapy
|
age: 55
gender: female
tissue: breast tumor
tumor biopsy acquisition: Such biopsy was taken from surgery specimen and selected by the pathologist in charge within 30 min. after tumor removal
treatment: A
sample_id: 08SE171
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM707580
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 13 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707580/suppl/GSM707580_08SE171HGU133Plus2.0_050608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM707581 | GPL570 |
|
Breast tumor biopsy_Postchemotherapy_08SE173
|
Breast tumor biopsy, Postchemotherapy
|
age: 48
gender: female
tissue: breast tumor
tumor biopsy acquisition: Such biopsy was taken from surgery specimen and selected by the pathologist in charge within 30 min. after tumor removal
treatment: B
sample_id: 08SE173
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM707581
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 13 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707581/suppl/GSM707581_08SE173HGU133Plus2.0_170608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM707582 | GPL570 |
|
Breast tumor biopsy_Postchemotherapy_08SE179
|
Breast tumor biopsy, Postchemotherapy
|
age: 58
gender: female
tissue: breast tumor
tumor biopsy acquisition: Such biopsy was taken from surgery specimen and selected by the pathologist in charge within 30 min. after tumor removal
treatment: C
sample_id: 08SE179
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM707582
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 13 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707582/suppl/GSM707582_08SE179HGU133Plus2.0_050608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM707600 | GPL570 |
|
Breast tumor biopsy_Postchemotherapy_08SE189
|
Breast tumor biopsy, Postchemotherapy
|
age: 53
gender: female
tissue: breast tumor
tumor biopsy acquisition: Such biopsy was taken from surgery specimen and selected by the pathologist in charge within 30 min. after tumor removal
treatment: A
sample_id: 08SE189
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM707600
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 13 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707600/suppl/GSM707600_08SE189HGU133Plus2.0_170608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
|
GSM707601 | GPL570 |
|
Breast tumor biopsy_Postchemotherapy_08SE276+08SE277
|
Breast tumor biopsy, Postchemotherapy
|
age: 53
gender: female
tissue: breast tumor
tumor biopsy acquisition: Such biopsy was taken from surgery specimen and selected by the pathologist in charge within 30 min. after tumor removal
treatment: A
sample_id: 08SE276+08SE277
pathologic response to chemotherapy (miller & payne grade): 3
|
Affymetrix Standard Protocol
|
| Sample_geo_accession | GSM707601
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Apr 13 2011
| | Sample_last_update_date | Dec 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA processing: snap frozen in liquid nitrogen and preserved at -80ºC. Before RNA extraction protocol, samples were sectioned in a cryostat to evalute the celularity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using using an RNeasy minikit from Qiagen. 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 GeneChip IVT Labelling Kit (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 Partek Genomics Suite v7.3.1 (Partek). Data were filtered again and a lineal regression model was applied to detect significant differences in gene expression between groups. Expression ratios of the differentially expressed genes are presented as fold changes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,,Vera
| | Sample_contact_email | lvera@correo.ugr.es
| | Sample_contact_phone | +34953220306
| | Sample_contact_department | Department of Oncology
| | Sample_contact_institute | Hospital Medico-Quirurgico de Jaen
| | Sample_contact_address | Avenida del Ejercito Español 10
| | Sample_contact_city | Jaen
| | Sample_contact_state | Jaen
| | Sample_contact_zip/postal_code | 23007
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707601/suppl/GSM707601_08SE276_08SE277HGU133Plus2.0_170608.CEL.gz
| | Sample_series_id | GSE28583
| | Sample_series_id | GSE28844
| | Sample_data_row_count | 54675
| | |
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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