Search results for the GEO ID: GSE23994  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM591056 | GPL570 |
|
Normal_epithelial_1
|
breast epithelial cells
|
phenotype: normal
ID: na
cell type: epithelial
|
|
| Sample_geo_accession | GSM591056
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591056/suppl/GSM591056.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591056/suppl/GSM591056.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591057 | GPL570 |
|
Normal_epithelial_2
|
breast epithelial cells
|
phenotype: normal
ID: na
cell type: epithelial
|
|
| Sample_geo_accession | GSM591057
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591057/suppl/GSM591057.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591057/suppl/GSM591057.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591058 | GPL570 |
|
Normal_epithelial_3
|
breast epithelial cells
|
phenotype: normal
ID: na
cell type: epithelial
|
|
| Sample_geo_accession | GSM591058
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591058/suppl/GSM591058.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591058/suppl/GSM591058.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591059 | GPL570 |
|
Normal_epithelial_4
|
breast epithelial cells
|
phenotype: normal
ID: na
cell type: epithelial
|
|
| Sample_geo_accession | GSM591059
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591059/suppl/GSM591059.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591059/suppl/GSM591059.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591060 | GPL570 |
|
LiFraumeni_epithelial_50_1
|
breast epithelial cells
|
phenotype: Li-Fraumeni
ID: 50
cell type: epithelial
|
|
| Sample_geo_accession | GSM591060
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591060/suppl/GSM591060.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591060/suppl/GSM591060.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591061 | GPL570 |
|
LiFraumeni_epithelial_50_2
|
breast epithelial cells
|
phenotype: Li-Fraumeni
ID: 50
cell type: epithelial
|
|
| Sample_geo_accession | GSM591061
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591061/suppl/GSM591061.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591061/suppl/GSM591061.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591062 | GPL570 |
|
LiFraumeni_epithelial_50_3
|
breast epithelial cells
|
phenotype: Li-Fraumeni
ID: 50
cell type: epithelial
|
|
| Sample_geo_accession | GSM591062
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591062/suppl/GSM591062.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591062/suppl/GSM591062.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591063 | GPL570 |
|
LiFraumeni_epithelial_50_4
|
breast epithelial cells
|
phenotype: Li-Fraumeni
ID: 50
cell type: epithelial
|
|
| Sample_geo_accession | GSM591063
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591063/suppl/GSM591063.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591063/suppl/GSM591063.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591064 | GPL570 |
|
LiFraumeni_epithelial_IUSM_1
|
breast epithelial cells
|
phenotype: Li-Fraumeni
ID: IUSM
cell type: epithelial
|
|
| Sample_geo_accession | GSM591064
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591064/suppl/GSM591064.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591064/suppl/GSM591064.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591065 | GPL570 |
|
LiFraumeni_epithelial_IUSM_2
|
breast epithelial cells
|
phenotype: Li-Fraumeni
ID: IUSM
cell type: epithelial
|
|
| Sample_geo_accession | GSM591065
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591065/suppl/GSM591065.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591065/suppl/GSM591065.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591066 | GPL570 |
|
LiFraumeni_epithelial_IUSM_3
|
breast epithelial cells
|
phenotype: Li-Fraumeni
ID: IUSM
cell type: epithelial
|
|
| Sample_geo_accession | GSM591066
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591066/suppl/GSM591066.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591066/suppl/GSM591066.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591067 | GPL570 |
|
LiFraumeni_epithelial_IUSM_4
|
breast epithelial cells
|
phenotype: Li-Fraumeni
ID: IUSM
cell type: epithelial
|
|
| Sample_geo_accession | GSM591067
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591067/suppl/GSM591067.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591067/suppl/GSM591067.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591068 | GPL570 |
|
Normal_stromal_1
|
breast stromal cells
|
phenotype: normal
ID: na
cell type: stromal
|
|
| Sample_geo_accession | GSM591068
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591068/suppl/GSM591068.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591068/suppl/GSM591068.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591069 | GPL570 |
|
Normal_stromal_2
|
breast stromal cells
|
phenotype: normal
ID: na
cell type: stromal
|
|
| Sample_geo_accession | GSM591069
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591069/suppl/GSM591069.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591069/suppl/GSM591069.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591070 | GPL570 |
|
Normal_stromal_3
|
breast stromal cells
|
phenotype: normal
ID: na
cell type: stromal
|
|
| Sample_geo_accession | GSM591070
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591070/suppl/GSM591070.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591070/suppl/GSM591070.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591071 | GPL570 |
|
Normal_stromal_4
|
breast stromal cells
|
phenotype: normal
ID: na
cell type: stromal
|
|
| Sample_geo_accession | GSM591071
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591071/suppl/GSM591071.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591071/suppl/GSM591071.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591072 | GPL570 |
|
LiFraumeni_stromal_50_1
|
breast stromal cells
|
phenotype: Li-Fraumeni
ID: 50
cell type: stromal
|
|
| Sample_geo_accession | GSM591072
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591072/suppl/GSM591072.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591072/suppl/GSM591072.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591073 | GPL570 |
|
LiFraumeni_stromal_50_2
|
breast stromal cells
|
phenotype: Li-Fraumeni
ID: 50
cell type: stromal
|
|
| Sample_geo_accession | GSM591073
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591073/suppl/GSM591073.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591073/suppl/GSM591073.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591074 | GPL570 |
|
LiFraumeni_stromal_50_3
|
breast stromal cells
|
phenotype: Li-Fraumeni
ID: 50
cell type: stromal
|
|
| Sample_geo_accession | GSM591074
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591074/suppl/GSM591074.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591074/suppl/GSM591074.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591075 | GPL570 |
|
LiFraumeni_stromal_50_4
|
breast stromal cells
|
phenotype: Li-Fraumeni
ID: 50
cell type: stromal
|
|
| Sample_geo_accession | GSM591075
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591075/suppl/GSM591075.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591075/suppl/GSM591075.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591076 | GPL570 |
|
LiFraumeni_stromal_IUSM_1
|
breast stromal cells
|
phenotype: Li-Fraumeni
ID: IUSM
cell type: stromal
|
|
| Sample_geo_accession | GSM591076
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591076/suppl/GSM591076.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591076/suppl/GSM591076.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591077 | GPL570 |
|
LiFraumeni_stromal_IUSM_2
|
breast stromal cells
|
phenotype: Li-Fraumeni
ID: IUSM
cell type: stromal
|
|
| Sample_geo_accession | GSM591077
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591077/suppl/GSM591077.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591077/suppl/GSM591077.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591078 | GPL570 |
|
LiFraumeni_stromal_IUSM_3
|
breast stromal cells
|
phenotype: Li-Fraumeni
ID: IUSM
cell type: stromal
|
|
| Sample_geo_accession | GSM591078
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591078/suppl/GSM591078.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591078/suppl/GSM591078.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
|
GSM591079 | GPL570 |
|
LiFraumeni_stromal_IUSM_4
|
breast stromal cells
|
phenotype: Li-Fraumeni
ID: IUSM
cell type: stromal
|
|
| Sample_geo_accession | GSM591079
| | Sample_status | Public on Oct 21 2010
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Oct 21 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All cells were tested at the same log phase of cell growth and at similar passages. Four independent cultures of each sample cell line were collected for RNA extraction. HME cells were cultured in modified basal medium 171 (Cascade Biologics, Portland, OR) supplemented with 0.5% bovine pituitary extract (Hammond Cell Technologies), 100 µg/ml epidermal growth factor (Invitrogen), 10 µg/ml insulin, 1 µg/ml hydrocortisone, 10 µg/ml transferrin (Sigma-Aldrich, St. Louis, MO). Medium was changed every 2-3 days. HMS cells were cultured as described in Shay et al., Mol Cell Biol. 1995;15:425-32].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using RNeasy mini-kit from Qiagen
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix Protocol for 3'IVT labeling from GeneChip® Expression Analysis Technical Manual
| | Sample_hyb_protocol | Arrays (HGU133 plus 2.0) were hybridized for 17h at 42oC.
| | Sample_scan_protocol | The arrays were washed and stained protocol by fluidics stations controlled by GCOS software using the standard Affymetrix protocol.
| | Sample_data_processing | The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Brittney-Shea,,Herbert
| | Sample_contact_email | brherber@iupui.edu
| | Sample_contact_department | Medical & Molecular Genetics
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 975 W. Walnut st.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591079/suppl/GSM591079.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591079/suppl/GSM591079.CHP.gz
| | Sample_series_id | GSE23994
| | Sample_data_row_count | 54675
| | |
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