Search results for the GEO ID: GSE23399  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM573832 | GPL570 |
|
no treatment , biological rep1
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Vehicle
time: control
|
Vehicle-1
|
| Sample_geo_accession | GSM573832
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573832/suppl/GSM573832.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573832/suppl/GSM573832.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573833 | GPL570 |
|
no treatment , biological rep2
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Vehicle
time: control
|
Vehicle-2
|
| Sample_geo_accession | GSM573833
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573833/suppl/GSM573833.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573833/suppl/GSM573833.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573834 | GPL570 |
|
paclitaxol treated,collect RNA at day 1 ,rep1
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Paclitaxol
time: day 1
|
Paclitaxol-Day1-1
|
| Sample_geo_accession | GSM573834
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573834/suppl/GSM573834.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573834/suppl/GSM573834.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573835 | GPL570 |
|
paclitaxol treated,collect RNA at day 1 ,rep2
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Paclitaxol
time: day 1
|
Paclitaxol-Day1-2
|
| Sample_geo_accession | GSM573835
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573835/suppl/GSM573835.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573835/suppl/GSM573835.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573836 | GPL570 |
|
paclitaxol treated,collect RNA at day 3 ,rep1
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Paclitaxol
time: day 3
|
Paclitaxol-Day3-1
|
| Sample_geo_accession | GSM573836
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573836/suppl/GSM573836.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573836/suppl/GSM573836.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573837 | GPL570 |
|
paclitaxol treated,collect RNA at day 3 ,rep2
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Paclitaxol
time: day 3
|
Paclitaxol-Day3-2
|
| Sample_geo_accession | GSM573837
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573837/suppl/GSM573837.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573837/suppl/GSM573837.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573838 | GPL570 |
|
paclitaxol treated,collect RNA at day 7 ,rep1
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Paclitaxol
time: day 7
|
Paclitaxol-Day7-1
|
| Sample_geo_accession | GSM573838
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573838/suppl/GSM573838.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573838/suppl/GSM573838.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573839 | GPL570 |
|
paclitaxol treated,collect RNA at day 7 ,rep2
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Paclitaxol
time: day 7
|
Paclitaxol-Day7-2
|
| Sample_geo_accession | GSM573839
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573839/suppl/GSM573839.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573839/suppl/GSM573839.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573840 | GPL570 |
|
doxorubicin treated,collect RNA at day 1 ,rep1
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Doxorubicin
time: day 1
|
Doxorubicin-Day1-1
|
| Sample_geo_accession | GSM573840
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573840/suppl/GSM573840.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573840/suppl/GSM573840.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573841 | GPL570 |
|
doxorubicin treated,collect RNA at day 1 ,rep2
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Doxorubicin
time: day 1
|
Doxorubicin-Day1-2
|
| Sample_geo_accession | GSM573841
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573841/suppl/GSM573841.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573841/suppl/GSM573841.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573842 | GPL570 |
|
doxorubicin treated,collect RNA at day 3 ,rep1
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Doxorubicin
time: day 3
|
Doxorubicin-Day3-1
|
| Sample_geo_accession | GSM573842
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573842/suppl/GSM573842.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573842/suppl/GSM573842.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573843 | GPL570 |
|
doxorubicin treated,collect RNA at day 3 ,rep2
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Doxorubicin
time: day 3
|
Doxorubicin-Day3-2
|
| Sample_geo_accession | GSM573843
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573843/suppl/GSM573843.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573843/suppl/GSM573843.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573844 | GPL570 |
|
doxorubicin treated,collect RNA at day 7 ,rep1
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Doxorubicin
time: day 7
|
Doxorubicin-Day7-1
|
| Sample_geo_accession | GSM573844
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573844/suppl/GSM573844.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573844/suppl/GSM573844.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
GSM573845 | GPL570 |
|
doxorubicin treated,collect RNA at day 7 ,rep2
|
Breast associatd fibroblasts
|
age: 59 years old
tissue: Breast
cell type: Breast cancer associated fibroblasts (BCAFs)
agent: Doxorubicin
time: day 7
|
Doxorubicin-Day7-2
|
| Sample_geo_accession | GSM573845
| | Sample_status | Public on Aug 03 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Aug 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Early-passage (passage 4-6) breast CAFs were treated with doxorubicin (Sigma) at 50 nM for 96 hours or paclitaxel (Sigma) at 0.65 μM for 24 hours. After completion of the treatments the cells were washed twice with PBS, replenished with drug-free culture medium and the cultures were maintained until subsequent analysis.
| | Sample_growth_protocol_ch1 | The BCAFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA samples were extracted from doxorubicin- , paclitaxel- or vehicle-treated breast CAFs using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jimmy,Jiun-Ming,Su
| | Sample_contact_email | jimmy.su.js@gmail.com
| | Sample_contact_phone | +886-6-208-3422 65246
| | Sample_contact_department | National Institute of Cancer Research
| | Sample_contact_institute | National Health Research Institutes,Taiwan
| | Sample_contact_address | 1F,No 367,Sheng-Li Rd. North District
| | Sample_contact_city | Tainan city
| | Sample_contact_state | n/a
| | Sample_contact_zip/postal_code | 70456
| | Sample_contact_country | Taiwan
| | Sample_contact_web_link | none
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573845/suppl/GSM573845.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573845/suppl/GSM573845.CHP.gz
| | Sample_series_id | GSE23399
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
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