Search results for the GEO ID: GSE27444  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM678312 | GPL570 |
|
Control, 1st infection
|
MCF7
|
retroviral transduction: control
|
Control.b1
fulvestrant sensitive MCF7 clone retroviraly induced with control plasmid encoding only the NF-kappaB p65 activation domain, 1st infection
|
| Sample_geo_accession | GSM678312
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678312/suppl/GSM678312.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678313 | GPL570 |
|
ZF-TF 115, 1st infection
|
MCF7
|
retroviral transduction: zinc finger transcription factor 115
|
ZF-TF.115.b1
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 115, 1st infection
|
| Sample_geo_accession | GSM678313
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678313/suppl/GSM678313.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678314 | GPL570 |
|
ZF-TF 19, 1st infection
|
MCF7
|
retroviral transduction: zinc finger transcription factor 19
|
ZF-TF.19.b1
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 19, 1st infection
|
| Sample_geo_accession | GSM678314
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678314/suppl/GSM678314.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678315 | GPL570 |
|
ZF-TF 64, 1st infection
|
MCF7
|
retroviral transduction: zinc finger transcription factor 64
|
ZF-TF.64.b1
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 64, 1st infection
|
| Sample_geo_accession | GSM678315
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678315/suppl/GSM678315.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678316 | GPL570 |
|
ZF-TF 70, 1st infection
|
MCF7
|
retroviral transduction: zinc finger transcription factor 70
|
ZF-TF.70.b1
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 70, 1st infection
|
| Sample_geo_accession | GSM678316
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678316/suppl/GSM678316.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678317 | GPL570 |
|
ZF-TF 7, 1st infection
|
MCF7
|
retroviral transduction: zinc finger transcription factor 7
|
ZF-TF.7.b1
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 7, 1st infection
|
| Sample_geo_accession | GSM678317
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678317/suppl/GSM678317.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678318 | GPL570 |
|
ZF-TF 83, 1st infection
|
MCF7
|
retroviral transduction: zinc finger transcription factor 83
|
ZF-TF.83.b1
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 83, 1st infection
|
| Sample_geo_accession | GSM678318
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678318/suppl/GSM678318.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678319 | GPL570 |
|
ZF-TF 115, 2nd infection
|
MCF7
|
retroviral transduction: zinc finger transcription factor 115
|
ZF-TF.115.b3
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 115, 2nd infection
|
| Sample_geo_accession | GSM678319
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678319/suppl/GSM678319.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678320 | GPL570 |
|
ZF-TF 19, 2nd infection
|
MCF7
|
retroviral transduction: zinc finger transcription factor 19
|
ZF-TF.19.b3
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 19, 2nd infection
|
| Sample_geo_accession | GSM678320
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678320/suppl/GSM678320.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678321 | GPL570 |
|
Control, 2nd infection
|
MCF7
|
retroviral transduction: control
|
Control.b3
fulvestrant sensitive MCF7 clone retroviraly induced with control plasmid encoding only the NF-kappaB p65 activation domain, 2nd infection
|
| Sample_geo_accession | GSM678321
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678321/suppl/GSM678321.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678322 | GPL570 |
|
ZF-TF 64, 2nd infection
|
MCF7
|
retroviral transduction: zinc finger transcription factor 64
|
ZF-TF.64.b4
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 64, 2nd infection
|
| Sample_geo_accession | GSM678322
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678322/suppl/GSM678322.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678323 | GPL570 |
|
ZF-TF 70, 2nd infection
|
MCF7
|
retroviral transduction: zinc finger transcription factor 70
|
ZF-TF.70.b3
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 70, 2nd infection
|
| Sample_geo_accession | GSM678323
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678323/suppl/GSM678323.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678324 | GPL570 |
|
ZF-TF 7, 2nd infection
|
MCF7
|
retroviral transduction: zinc finger transcription factor 7
|
ZF-TF.7.b4
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 7, 2nd infection
|
| Sample_geo_accession | GSM678324
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678324/suppl/GSM678324.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
| | |
|
GSM678325 | GPL570 |
|
ZF-TF 83, 2nd infection
|
MCF7
|
retroviral transduction: zinc finger transcription factor 83
|
ZF-TF.83.b3
fulvestrant sensitive MCF7 clone retroviraly induced with zinc finger transcription factor 83, 2nd infection
|
| Sample_geo_accession | GSM678325
| | Sample_status | Public on Jul 18 2011
| | Sample_submission_date | Feb 22 2011
| | Sample_last_update_date | Jul 18 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 293T cells were seeded at 5 x 105 cells per 10 cm culture dish, transfected with 3.2 μg of ZT-TF p65 activator library DNA and 2.4μg and 0.8μg of PMD-MLV and PMD-G plasmid DNA using Fugene 6 according to the manufacture’s protocol and retroviral supernatant harvested 48 hrs later. MCF7-R73 cells (6 x105 per 10 cm plate) were infected with 1.33 x 105 ZF-TF retrovirions in media containing polybrene. Two days post-infection the cells were exposed to puromycin (0.4mg/ml), and three days later were subjected to continuous combined puromycin and fulvestrant (100nM) selection for an additional 42 days. Retroviral DNA was recovered by PCR, subcloned into the pDONOR plasmid using Gateway technology (Invitrogen), and subject to DNA sequencing that revealed 46 unique ZF-TF arrays. The 46 ZF-TFs were re-cloned into the retroviral destination plasmid using Gateway technology, 46 ZF-TF retroviral supernatants generated, and MCF-R73 cells infected and subjected to puromycin and fulvestrant selection. Six unique ZF-TFs conferred drug resistance in the presence of continuous fulvestrant exposure. A control MCF7 cell line (MCF7-R238) was generated by infecting MCF7-R73 cells with a retrovirus bearing the p65 activation domain only. T47D cells were infected with the six unique ZF-TF bearing retroviruses and subjected to fulvestrant exposure as described for the MCF7 cells.
| | Sample_growth_protocol_ch1 | MCF7-R73 cells, a clonal isolate derived from the MCF7 cell line were kindly provided by Dr. Toshi Shioda (MGH, Charlestown, MA) and maintained in a xenoestrogen controlled environment as described in Coser KR, Wittner BS, Rosenthal NF, Collins SC, Melas A, et al. (2009) Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common monoclonal drug-resistant progenitor, Proc Natl Acad Sci U S A 106: 14536-14541
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100. The expression values were corrected for batch effect on a per-probe-set basis as follows. For each batch N other than the first, we added to the expression values of batch N the difference between the average expression value on the first batch and the average expression value on batch N.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM678nnn/GSM678325/suppl/GSM678325.CEL.gz
| | Sample_series_id | GSE27444
| | Sample_data_row_count | 54675
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