Search results for the GEO ID: GSE27220  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM672818 | GPL570 |
|
Breast cancer_Control_24h_6A
|
tissue, breast cancer, control, 24h
|
disease state: Breast cancer
agent: none
gender: female
age: 70
histologic type: CDI
clinical stage: III
|
Organotypic culture_ Breast cancer_Control_6
|
| Sample_geo_accession | GSM672818
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672818/suppl/GSM672818.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672819 | GPL570 |
|
Breast cancer_Control_24h_11A
|
tissue, breast cancer, control, 24h
|
disease state: Breast cancer
agent: none
gender: female
age: 74
histologic type: CDI
clinical stage: III
|
Organotypic culture_ Breast cancer_Control_11
|
| Sample_geo_accession | GSM672819
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672819/suppl/GSM672819.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672820 | GPL570 |
|
Breast cancer_Control_24h_12A
|
tissue, breast cancer, control, 24h
|
disease state: Breast cancer
agent: none
gender: female
age: 56
histologic type: CDI
clinical stage: I
|
Organotypic culture_ Breast cancer_Control_12
|
| Sample_geo_accession | GSM672820
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672820/suppl/GSM672820.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672821 | GPL570 |
|
Breast cancer_Control_24h_13A
|
tissue, breast cancer, control, 24h
|
disease state: Breast cancer
agent: none
gender: female
age: 56
histologic type: CDI
clinical stage: II
|
Organotypic culture_ Breast cancer_Control_13
|
| Sample_geo_accession | GSM672821
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672821/suppl/GSM672821.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672822 | GPL570 |
|
Breast cancer_Control_24h_15A
|
tissue, breast cancer, control, 24h
|
disease state: Breast cancer
agent: none
gender: female
age: 76
histologic type: CDI
clinical stage: III
|
Organotypic culture_ Breast cancer_Control_15
|
| Sample_geo_accession | GSM672822
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672822/suppl/GSM672822.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672823 | GPL570 |
|
Breast cancer_VitaminD_0.5nM_24h_6B
|
tissue, breast cancer, vitaminD 0.5nM, 24h
|
disease state: Breast cancer
agent: VitaminD_0.5nM
gender: female
age: 70
histologic type: CDI
clinical stage: III
|
Organotypic culture_ Breast cancer_VitaminD_0.5nM_6
|
| Sample_geo_accession | GSM672823
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672823/suppl/GSM672823.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672824 | GPL570 |
|
Breast cancer_VitaminD_0.5nM_24h_11B
|
tissue, breast cancer, vitaminD 0.5nM, 24h
|
disease state: Breast cancer
agent: VitaminD_0.5nM
gender: female
age: 74
histologic type: CDI
clinical stage: III
|
Organotypic culture_ Breast cancer_VitaminD_0.5nM_11
|
| Sample_geo_accession | GSM672824
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672824/suppl/GSM672824.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672825 | GPL570 |
|
Breast cancer_VitaminD_0.5nM_24h_12B
|
tissue, breast cancer, vitaminD 0.5nM, 24h
|
disease state: Breast cancer
agent: VitaminD_0.5nM
gender: female
age: 56
histologic type: CDI
clinical stage: I
|
Organotypic culture_ Breast cancer_VitaminD_0.5nM_12
|
| Sample_geo_accession | GSM672825
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672825/suppl/GSM672825.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672826 | GPL570 |
|
Breast cancer_VitaminD_0.5nM_24h_13B
|
tissue, breast cancer, vitaminD 0.5nM, 24h
|
disease state: Breast cancer
agent: VitaminD_0.5nM
gender: female
age: 56
histologic type: CDI
clinical stage: II
|
Organotypic culture_ Breast cancer_VitaminD_0.5nM_13
|
| Sample_geo_accession | GSM672826
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672826/suppl/GSM672826.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672827 | GPL570 |
|
Breast cancer_VitaminD_0.5nM_24h_15B
|
tissue, breast cancer, vitaminD 0.5nM, 24h
|
disease state: Breast cancer
agent: VitaminD_0.5nM
gender: female
age: 76
histologic type: CDI
clinical stage: III
|
Organotypic culture_ Breast cancer_VitaminD_0.5nM_15
|
| Sample_geo_accession | GSM672827
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672827/suppl/GSM672827.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672828 | GPL570 |
|
Breast cancer_VitaminD_100nM_24h_6C
|
tissue, breast cancer, vitaminD 100nM, 24h
|
disease state: Breast cancer
agent: VitaminD_100nM
gender: female
age: 70
histologic type: CDI
clinical stage: III
|
Organotypic culture_ Breast cancer_VitaminD_100nM_6
|
| Sample_geo_accession | GSM672828
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672828/suppl/GSM672828.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672829 | GPL570 |
|
Breast cancer_VitaminD_100nM_24h_11C
|
tissue, breast cancer, vitaminD 100nM, 24h
|
disease state: Breast cancer
agent: VitaminD_100nM
gender: female
age: 74
histologic type: CDI
clinical stage: III
|
Organotypic culture_ Breast cancer_VitaminD_100nM_11
|
| Sample_geo_accession | GSM672829
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672829/suppl/GSM672829.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672830 | GPL570 |
|
Breast cancer_VitaminD_100nM_24h_12C
|
tissue, breast cancer, vitaminD 100nM, 24h
|
disease state: Breast cancer
agent: VitaminD_100nM
gender: female
age: 56
histologic type: CDI
clinical stage: I
|
Organotypic culture_ Breast cancer_VitaminD_100nM_12
|
| Sample_geo_accession | GSM672830
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672830/suppl/GSM672830.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672831 | GPL570 |
|
Breast cancer_VitaminD_100nM_24h_13C
|
tissue, breast cancer, vitaminD 100nM, 24h
|
disease state: Breast cancer
agent: VitaminD_100nM
gender: female
age: 56
histologic type: CDI
clinical stage: II
|
Organotypic culture_ Breast cancer_VitaminD_100nM_13
|
| Sample_geo_accession | GSM672831
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672831/suppl/GSM672831.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
|
GSM672832 | GPL570 |
|
Breast cancer_VitaminD_100nM_24h_15C
|
tissue, breast cancer, vitaminD 100nM, 24h
|
disease state: Breast cancer
agent: VitaminD_100nM
gender: female
age: 76
histologic type: CDI
clinical stage: III
|
Organotypic culture_ Breast cancer_VitaminD_100nM_15
|
| Sample_geo_accession | GSM672832
| | Sample_status | Public on Feb 11 2011
| | Sample_submission_date | Feb 10 2011
| | Sample_last_update_date | Feb 11 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Organotypic culture protocol: Tumor fragments were obtained immediately after tumor resection by the pathologist, who selected an involved area. Fragments were than placed into culture medium (RPMI 1640 with antibiotics and fungicide). Tissue slices were prepared using the Krumdieck tissue slicing system (Alabama Research and Development Corporation, Birmingham, AL, USA). Fragment thickness varied between 400-800μm. Slices were cultured for 24 hours in 6-well plates (1 slice/well; 1-3 slices per treatment) containing 2 mL of culture media, RPMI supplemented with 10% v/v FBS, antibiotics and 0.001% ethanol (vehicle) or 1,25(OH)2D3 (Calbiochem, Darmstadt, Germany) 0.5nM or 100nM (from now on called physiological and supra-physiological concentrations, respectively).
| | Sample_extract_protocol_ch1 | Tumor specimens were pulverized (Bio-PulverizerTM BioSpec Products Inc., Oklahoma, USA) under liquid nitrogen and total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA, USA), according to the manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | two-round linear amplification was carried out according to Affymetrix protocol (Two Cycle Target Labeling Kit, Affymetrix, Santa Clara, CA, USA). Afterwards, biotin-labeled cRNA was synthesized from double strand cDNA, using IVT labeling kit (Affymetrix) and 20 µg of biotinylated were fragmented cRNA.
| | Sample_hyb_protocol | After hybridization cocktails preparation, the Affymetrix Human Genome U133 Plus 2.0 GeneChip array was hybridized with 15 mg of biotin-labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual (2005-2006)
| | Sample_scan_protocol | GeneChips, bound to streptavidin-biotin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Affymetrix GeneChip Scanner 3000 G7
| | Sample_data_processing | Data were analysed using Robust Multichip Averaging (RMA) algorithm which is based on perfect match intensity probe and quantile normalization method available GeneSpring GX software.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Lucia,Hirata,Katayama
| | Sample_contact_email | lucia@lim24.fm.usp.br
| | Sample_contact_phone | (55)(11)30617164
| | Sample_contact_fax | (55)(11)30826580
| | Sample_contact_laboratory | Oncology
| | Sample_contact_department | Radiology and Oncology
| | Sample_contact_institute | Faculty of Medicine University São Paulo
| | Sample_contact_address | Av Dr Arnaldo
| | Sample_contact_city | São Paulo
| | Sample_contact_state | São Paulo
| | Sample_contact_zip/postal_code | 01264903
| | Sample_contact_country | Brazil
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672832/suppl/GSM672832.CEL.gz
| | Sample_series_id | GSE27220
| | Sample_data_row_count | 54675
| | |
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