Search results for the GEO ID: GSE13787  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM346882 | GPL570 |
|
Breast cancer basal 1
|
Breast sample
|
Gender: female
subtype: basal-like
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346882
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Sep 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346882/suppl/GSM346882.CEL.gz
| | Sample_relation | Reanalyzed by: GSE31519
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346883 | GPL570 |
|
Breast cancer basal 2
|
Breast sample
|
Gender: female
subtype: basal-like
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346883
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Sep 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346883/suppl/GSM346883.CEL.gz
| | Sample_relation | Reanalyzed by: GSE31519
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346884 | GPL570 |
|
Breast cancer basal 4
|
Breast sample
|
Gender: female
subtype: basal-like
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346884
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Sep 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346884/suppl/GSM346884.CEL.gz
| | Sample_relation | Reanalyzed by: GSE31519
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346885 | GPL570 |
|
Breast cancer basal 7
|
Breast sample
|
Gender: female
subtype: basal-like
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346885
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Sep 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346885/suppl/GSM346885.CEL.gz
| | Sample_relation | Reanalyzed by: GSE31519
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346886 | GPL570 |
|
Breast cancer basal 8
|
Breast sample
|
Gender: female
subtype: basal-like
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346886
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Sep 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346886/suppl/GSM346886.CEL.gz
| | Sample_relation | Reanalyzed by: GSE31519
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346887 | GPL570 |
|
Breast cancer basal 9
|
Breast sample
|
Gender: female
subtype: basal-like
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346887
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346887/suppl/GSM346887.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346888 | GPL570 |
|
Breast cancer basal 10
|
Breast sample
|
Gender: female
subtype: basal-like
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346888
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346888/suppl/GSM346888.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346889 | GPL570 |
|
Breast cancer basal 11
|
Breast sample
|
Gender: female
subtype: basal-like
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346889
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Sep 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346889/suppl/GSM346889.CEL.gz
| | Sample_relation | Reanalyzed by: GSE31519
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346890 | GPL570 |
|
Breast cancer basal 12
|
Breast sample
|
Gender: female
subtype: basal-like
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346890
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Sep 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346890/suppl/GSM346890.CEL.gz
| | Sample_relation | Reanalyzed by: GSE31519
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346891 | GPL570 |
|
Breast cancer basal 18
|
Breast sample
|
Gender: female
subtype: basal-like
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346891
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346891/suppl/GSM346891.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346892 | GPL570 |
|
Breast cancer basal 20
|
Breast sample
|
Gender: female
subtype: basal-like
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346892
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Sep 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346892/suppl/GSM346892.CEL.gz
| | Sample_relation | Reanalyzed by: GSE31519
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346893 | GPL570 |
|
Breast cancer basal 21
|
Breast sample
|
Gender: female
subtype: basal-like
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346893
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346893/suppl/GSM346893.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346894 | GPL570 |
|
Breast cancer her2+ 3
|
Breast sample
|
Gender: female
subtype: her2+
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346894
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346894/suppl/GSM346894.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346895 | GPL570 |
|
Breast cancer her2+ 5
|
Breast sample
|
Gender: female
subtype: her2+
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346895
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346895/suppl/GSM346895.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346896 | GPL570 |
|
Breast cancer her2+ 6
|
Breast sample
|
Gender: female
subtype: her2+
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346896
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346896/suppl/GSM346896.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346897 | GPL570 |
|
Breast cancer her2+ 13
|
Breast sample
|
Gender: female
subtype: her2+
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346897
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346897/suppl/GSM346897.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346898 | GPL570 |
|
Breast cancer her2+ 15
|
Breast sample
|
Gender: female
subtype: her2+
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346898
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346898/suppl/GSM346898.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346899 | GPL570 |
|
Breast cancer her2+ 16
|
Breast sample
|
Gender: female
subtype: her2+
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346899
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346899/suppl/GSM346899.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346900 | GPL570 |
|
Breast cancer her2+ 17
|
Breast sample
|
Gender: female
subtype: her2+
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346900
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Sep 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346900/suppl/GSM346900.CEL.gz
| | Sample_relation | Reanalyzed by: GSE31519
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346901 | GPL570 |
|
Breast cancer her2+ 19
|
Breast sample
|
Gender: female
subtype: her2+
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346901
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346901/suppl/GSM346901.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346902 | GPL570 |
|
Breast cancer her2+ 23
|
Breast sample
|
Gender: female
subtype: her2+
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346902
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346902/suppl/GSM346902.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346903 | GPL570 |
|
Breast cancer her2+ 24
|
Breast sample
|
Gender: female
subtype: her2+
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346903
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Dec 02 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346903/suppl/GSM346903.CEL.gz
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
|
GSM346904 | GPL570 |
|
Breast cancer her2+ 25
|
Breast sample
|
Gender: female
subtype: her2+
Grade: III
|
All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification
|
| Sample_geo_accession | GSM346904
| | Sample_status | Public on Dec 03 2008
| | Sample_submission_date | Dec 02 2008
| | Sample_last_update_date | Sep 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Institut Curie, Centre de Ressources Biologiques, Paris, France
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was done using RNAeasy minikit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the IVT reaction. The labelled cRNA was then cleaned up and fragmented
| | Sample_hyb_protocol | 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin
| | Sample_scan_protocol | Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA)
| | Sample_data_processing | Background correction method: GC Robust Mult-array Average (GC-RMA).
| | Sample_data_processing | Normalization: quantile
| | Sample_data_processing | Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
| | Sample_data_processing | Signal intensities were log2-transformed
| | Sample_platform_id | GPL570
| | Sample_contact_name | Thierry,,Dubois
| | Sample_contact_email | thierry.dubois@curie.fr
| | Sample_contact_phone | 33(0)153197416
| | Sample_contact_fax | 33(0)153197418
| | Sample_contact_laboratory | Laboratoire de Signalisation
| | Sample_contact_department | Département de Transfert
| | Sample_contact_institute | Institut Curie
| | Sample_contact_address | 26 rue d'Ulm
| | Sample_contact_city | Paris
| | Sample_contact_zip/postal_code | 75005
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346904/suppl/GSM346904.CEL.gz
| | Sample_relation | Reanalyzed by: GSE31519
| | Sample_series_id | GSE13787
| | Sample_data_row_count | 54613
| | |
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