Search results for the GEO ID: GSE35925  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM877494 | GPL570 |
|
Breast cancer_Control_15_Pre
|
tissue, breast cancer, control
|
gender: female
age: 54
histologic type: metaplastic
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877494
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877494/suppl/GSM877494_c1_15CA.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877495 | GPL570 |
|
Breast cancer_1,25(OH)2D3_15_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 54
histologic type: metaplastic
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877495
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877495/suppl/GSM877495_t1_15CAT.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877496 | GPL570 |
|
Breast cancer_Control_16_Pre
|
tissue, breast cancer, control
|
gender: female
age: 62
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877496
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877496/suppl/GSM877496_16CA_210509.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877497 | GPL570 |
|
Breast cancer_1,25(OH)2D3_16_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 62
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877497
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877497/suppl/GSM877497_16CAT_2_030409.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877498 | GPL570 |
|
Breast cancer_Control_17_Pre
|
tissue, breast cancer, control
|
gender: female
age: 63
histologic type: CLI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877498
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877498/suppl/GSM877498_17CA_2_030409.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877499 | GPL570 |
|
Breast cancer_1,25(OH)2D3_17_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 63
histologic type: CLI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877499
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877499/suppl/GSM877499_17CAT_2_030409.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877500 | GPL570 |
|
Breast cancer_Control_21_Pre
|
tissue, breast cancer, control
|
gender: female
age: 49
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877500
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877500/suppl/GSM877500_21CA_250909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877501 | GPL570 |
|
Breast cancer_1,25(OH)2D3_21_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 49
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877501
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877501/suppl/GSM877501_21CAT_250909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877502 | GPL570 |
|
Breast cancer_Control_26_Pre
|
tissue, breast cancer, control
|
gender: female
age: 49
histologic type: CLI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877502
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877502/suppl/GSM877502_26CA_-081009.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877503 | GPL570 |
|
Breast cancer_1,25(OH)2D3_26_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 49
histologic type: CLI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877503
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877503/suppl/GSM877503_26CAT-081009.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877504 | GPL570 |
|
Breast cancer_Control_27_Pre
|
tissue, breast cancer, control
|
gender: female
age: 66
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877504
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877504/suppl/GSM877504_27CA_290909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877505 | GPL570 |
|
Breast cancer_1,25(OH)2D3_27_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 66
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877505
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877505/suppl/GSM877505_27CAT_290909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877506 | GPL570 |
|
Breast cancer_Control_29_Pre
|
tissue, breast cancer, control
|
gender: female
age: 56
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877506
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877506/suppl/GSM877506_29CA_250909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877507 | GPL570 |
|
Breast cancer_1,25(OH)2D3_29_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 56
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877507
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877507/suppl/GSM877507_29CAT_250909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877508 | GPL570 |
|
Breast cancer_Control_30_Pre
|
tissue, breast cancer, control
|
gender: female
age: 62
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877508
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877508/suppl/GSM877508_30CA_290909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877509 | GPL570 |
|
Breast cancer_1,25(OH)2D3_30_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 62
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877509
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877509/suppl/GSM877509_30CAT_290909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877510 | GPL570 |
|
Breast cancer_Control_33_Pre
|
tissue, breast cancer, control
|
gender: female
age: 52
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877510
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877510/suppl/GSM877510_33CA_250909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877511 | GPL570 |
|
Breast cancer_1,25(OH)2D3_33_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 52
histologic type: CDI/CLI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877511
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877511/suppl/GSM877511_33CAT_250909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877512 | GPL570 |
|
Breast cancer_Control_34_Pre
|
tissue, breast cancer, control
|
gender: female
age: 63
histologic type: CDICLI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877512
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877512/suppl/GSM877512_34CA-081009.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877513 | GPL570 |
|
Breast cancer_1,25(OH)2D3_34_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 63
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877513
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877513/suppl/GSM877513_34CAT-081009.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877514 | GPL570 |
|
Breast cancer_Control_35_Pre
|
tissue, breast cancer, control
|
gender: female
age: 66
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877514
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877514/suppl/GSM877514_35CA_250909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877515 | GPL570 |
|
Breast cancer_1,25(OH)2D3_35_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 66
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877515
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877515/suppl/GSM877515_35CAT_250909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877516 | GPL570 |
|
Breast cancer_Control_36_Pre
|
tissue, breast cancer, control
|
gender: female
age: 51
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877516
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877516/suppl/GSM877516_36CA_28102009.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877517 | GPL570 |
|
Breast cancer_1,25(OH)2D3_36_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 51
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877517
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877517/suppl/GSM877517_36CAT_28102009.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877518 | GPL570 |
|
Breast cancer_Control_41_Pre
|
tissue, breast cancer, control
|
gender: female
age: 66
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877518
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877518/suppl/GSM877518_41CA_290909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877519 | GPL570 |
|
Breast cancer_1,25(OH)2D3_41_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 66
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877519
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877519/suppl/GSM877519_41CAT_290909.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877520 | GPL570 |
|
Breast cancer_Control_42_Pre
|
tissue, breast cancer, control
|
gender: female
age: 64
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877520
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877520/suppl/GSM877520_42CA.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877521 | GPL570 |
|
Breast cancer_1,25(OH)2D3_42_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 64
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877521
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877521/suppl/GSM877521_42CAT_161009.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877522 | GPL570 |
|
Breast cancer_Control_43_Pre
|
tissue, breast cancer, control
|
gender: female
age: 66
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877522
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877522/suppl/GSM877522_43CA_161009.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
|
GSM877523 | GPL570 |
|
Breast cancer_1,25(OH)2D3_43_Post
|
tissue, breast cancer, calcitriol
|
gender: female
age: 66
histologic type: CDI
tissue type: breast cancer
|
|
| Sample_geo_accession | GSM877523
| | Sample_status | Public on Feb 18 2012
| | Sample_submission_date | Feb 17 2012
| | Sample_last_update_date | Feb 18 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Organotypic culture protocol: Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tissue 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. RNA integrity was verified in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number > 4.8 (RIN, median value: 8.4) were analyzed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Beginning with 100 ng total RNA, 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 | Analysis to generate report files for quality control. Background correction, normalization and summarization of raw data (CEL files) were performed using the Robust Multi-Array Average (RMA) method available on R package. Filtering was set to select 30% of genes with the highest standard deviation. Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software. Differential gene expression between post and pre-supplementation samples was assessed using two class paired Significance Analysis of Microarray (SAM). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV (MultiExperiment Viewer – Boston, MA, USA).
| | 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/GSM877nnn/GSM877523/suppl/GSM877523_43CAT_161009.CEL.gz
| | Sample_series_id | GSE35925
| | Sample_data_row_count | 54675
| | |
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