Search results for the GEO ID: GSE19445  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM484649 | GPL570 |
|
inhibitor_series-steadystate
|
LNCaP cells - steady state
|
cell line: LNCaP
protocol: steady state
|
LNCaP cells grown in RPMI supplemented with 10% FBS.
|
| Sample_geo_accession | GSM484649
| | Sample_status | Public on Jul 04 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Jun 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For sh-RNA knockdown experiments LNCaP cells were transfected with GFP expression vectors encoding shRNA specific to TOP2Β (sh-TOP2Β) or sh-control, deprived of androgen and then treated with DHT (100 nM) or vehicle control for 16 h. GFP positive cells were collected by FACS sorting and subjected to microarray analysis. For inhibitor experiments LNCaP cells were androgen-deprived (control), subsequently stimulated with 100 nM DHT for 16 h (DHT), or pretreated with 100 μM etoposide (DHT+ET) or 100 μM merbarone (DHT+Mer) for 2 h prior to DHT stimulation.
| | Sample_growth_protocol_ch1 = LNCaP cells were propagated in RPMI medium supplemented with 10% fetal bovine serum ( | steady state). In order to deplete cells of basal androgens, all cells were washed with serum-free medium 3 times for 1 h and incubated in 5% charcoal-stripped FBS containing medium for 48 h prior to experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cell lines using a RNeasy RNA extraction kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Samples were hybridized to HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) according to the manufacturer’s protocols at the Johns Hopkins Microarray facility.
| | Sample_scan_protocol | HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) were scanned on the Affymetrix GeneChip Scanner 3000 7G at the Johns Hopkins Microarray facility
| | Sample_data_processing | Data from all microarrays were preprocessed in a single batch using RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Aryee
| | Sample_contact_laboratory | Srinivasan Yegnasubramanian
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University School of Medicine
| | Sample_contact_address | 1650 Orleans St
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484649/suppl/GSM484649.CEL.gz
| | Sample_series_id | GSE19445
| | Sample_data_row_count | 54675
| | |
|
GSM484650 | GPL570 |
|
inhibitor_series-control
|
LNCaP cells - serum starved
|
cell line: LNCaP
protocol: androgen deprivation
|
Androgen deprivation.
|
| Sample_geo_accession | GSM484650
| | Sample_status | Public on Jul 04 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Jun 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For sh-RNA knockdown experiments LNCaP cells were transfected with GFP expression vectors encoding shRNA specific to TOP2Β (sh-TOP2Β) or sh-control, deprived of androgen and then treated with DHT (100 nM) or vehicle control for 16 h. GFP positive cells were collected by FACS sorting and subjected to microarray analysis. For inhibitor experiments LNCaP cells were androgen-deprived (control), subsequently stimulated with 100 nM DHT for 16 h (DHT), or pretreated with 100 μM etoposide (DHT+ET) or 100 μM merbarone (DHT+Mer) for 2 h prior to DHT stimulation.
| | Sample_growth_protocol_ch1 = LNCaP cells were propagated in RPMI medium supplemented with 10% fetal bovine serum ( | steady state). In order to deplete cells of basal androgens, all cells were washed with serum-free medium 3 times for 1 h and incubated in 5% charcoal-stripped FBS containing medium for 48 h prior to experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cell lines using a RNeasy RNA extraction kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Samples were hybridized to HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) according to the manufacturer’s protocols at the Johns Hopkins Microarray facility.
| | Sample_scan_protocol | HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) were scanned on the Affymetrix GeneChip Scanner 3000 7G at the Johns Hopkins Microarray facility
| | Sample_data_processing | Data from all microarrays were preprocessed in a single batch using RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Aryee
| | Sample_contact_laboratory | Srinivasan Yegnasubramanian
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University School of Medicine
| | Sample_contact_address | 1650 Orleans St
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484650/suppl/GSM484650.CEL.gz
| | Sample_series_id | GSE19445
| | Sample_data_row_count | 54675
| | |
|
GSM484651 | GPL570 |
|
inhibitor_series-DHT
|
LNCaP cells - DHT treated
|
cell line: LNCaP
protocol: androgen deprivation
agent: DHT
|
Androgen deprivation followed by DHT (100 nM) treatment for 16 h.
|
| Sample_geo_accession | GSM484651
| | Sample_status | Public on Jul 04 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Jun 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For sh-RNA knockdown experiments LNCaP cells were transfected with GFP expression vectors encoding shRNA specific to TOP2Β (sh-TOP2Β) or sh-control, deprived of androgen and then treated with DHT (100 nM) or vehicle control for 16 h. GFP positive cells were collected by FACS sorting and subjected to microarray analysis. For inhibitor experiments LNCaP cells were androgen-deprived (control), subsequently stimulated with 100 nM DHT for 16 h (DHT), or pretreated with 100 μM etoposide (DHT+ET) or 100 μM merbarone (DHT+Mer) for 2 h prior to DHT stimulation.
| | Sample_growth_protocol_ch1 = LNCaP cells were propagated in RPMI medium supplemented with 10% fetal bovine serum ( | steady state). In order to deplete cells of basal androgens, all cells were washed with serum-free medium 3 times for 1 h and incubated in 5% charcoal-stripped FBS containing medium for 48 h prior to experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cell lines using a RNeasy RNA extraction kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Samples were hybridized to HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) according to the manufacturer’s protocols at the Johns Hopkins Microarray facility.
| | Sample_scan_protocol | HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) were scanned on the Affymetrix GeneChip Scanner 3000 7G at the Johns Hopkins Microarray facility
| | Sample_data_processing | Data from all microarrays were preprocessed in a single batch using RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Aryee
| | Sample_contact_laboratory | Srinivasan Yegnasubramanian
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University School of Medicine
| | Sample_contact_address | 1650 Orleans St
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484651/suppl/GSM484651.CEL.gz
| | Sample_series_id | GSE19445
| | Sample_data_row_count | 54675
| | |
|
GSM484652 | GPL570 |
|
inhibitor_series-DHT+ET
|
LNCaP cells - DHT + Etoposide
|
cell line: LNCaP
protocol: androgen deprivation + Etoposide
agent: DHT
|
Androgen deprivation and etoposide 100 μM preterated (2 h) followed by DHT treatment (16 h).
|
| Sample_geo_accession | GSM484652
| | Sample_status | Public on Jul 04 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Jun 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For sh-RNA knockdown experiments LNCaP cells were transfected with GFP expression vectors encoding shRNA specific to TOP2Β (sh-TOP2Β) or sh-control, deprived of androgen and then treated with DHT (100 nM) or vehicle control for 16 h. GFP positive cells were collected by FACS sorting and subjected to microarray analysis. For inhibitor experiments LNCaP cells were androgen-deprived (control), subsequently stimulated with 100 nM DHT for 16 h (DHT), or pretreated with 100 μM etoposide (DHT+ET) or 100 μM merbarone (DHT+Mer) for 2 h prior to DHT stimulation.
| | Sample_growth_protocol_ch1 = LNCaP cells were propagated in RPMI medium supplemented with 10% fetal bovine serum ( | steady state). In order to deplete cells of basal androgens, all cells were washed with serum-free medium 3 times for 1 h and incubated in 5% charcoal-stripped FBS containing medium for 48 h prior to experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cell lines using a RNeasy RNA extraction kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Samples were hybridized to HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) according to the manufacturer’s protocols at the Johns Hopkins Microarray facility.
| | Sample_scan_protocol | HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) were scanned on the Affymetrix GeneChip Scanner 3000 7G at the Johns Hopkins Microarray facility
| | Sample_data_processing | Data from all microarrays were preprocessed in a single batch using RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Aryee
| | Sample_contact_laboratory | Srinivasan Yegnasubramanian
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University School of Medicine
| | Sample_contact_address | 1650 Orleans St
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484652/suppl/GSM484652.CEL.gz
| | Sample_series_id | GSE19445
| | Sample_data_row_count | 54675
| | |
|
GSM484653 | GPL570 |
|
inhibitor_series-DHT+MER
|
LNCaP cells - DHT + Merbarone
|
cell line: LNCaP
protocol: androgen deprivation + Merbarone
agent: DHT
|
Androgen deprivation and merbarone 100 μM preterated (2 h) followed by DHT treatment (16 h).
|
| Sample_geo_accession | GSM484653
| | Sample_status | Public on Jul 04 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Jun 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For sh-RNA knockdown experiments LNCaP cells were transfected with GFP expression vectors encoding shRNA specific to TOP2Β (sh-TOP2Β) or sh-control, deprived of androgen and then treated with DHT (100 nM) or vehicle control for 16 h. GFP positive cells were collected by FACS sorting and subjected to microarray analysis. For inhibitor experiments LNCaP cells were androgen-deprived (control), subsequently stimulated with 100 nM DHT for 16 h (DHT), or pretreated with 100 μM etoposide (DHT+ET) or 100 μM merbarone (DHT+Mer) for 2 h prior to DHT stimulation.
| | Sample_growth_protocol_ch1 = LNCaP cells were propagated in RPMI medium supplemented with 10% fetal bovine serum ( | steady state). In order to deplete cells of basal androgens, all cells were washed with serum-free medium 3 times for 1 h and incubated in 5% charcoal-stripped FBS containing medium for 48 h prior to experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cell lines using a RNeasy RNA extraction kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Samples were hybridized to HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) according to the manufacturer’s protocols at the Johns Hopkins Microarray facility.
| | Sample_scan_protocol | HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) were scanned on the Affymetrix GeneChip Scanner 3000 7G at the Johns Hopkins Microarray facility
| | Sample_data_processing | Data from all microarrays were preprocessed in a single batch using RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Aryee
| | Sample_contact_laboratory | Srinivasan Yegnasubramanian
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University School of Medicine
| | Sample_contact_address | 1650 Orleans St
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484653/suppl/GSM484653.CEL.gz
| | Sample_series_id | GSE19445
| | Sample_data_row_count | 54675
| | |
|
GSM484654 | GPL570 |
|
shrna_series-GFP
|
LNCaP cells - GFP only
|
cell line: LNCaP
protocol: control transfection and androgen deprivation
|
sh-control vector transfection and androgen deprivation.
|
| Sample_geo_accession | GSM484654
| | Sample_status | Public on Jul 04 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Jun 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For sh-RNA knockdown experiments LNCaP cells were transfected with GFP expression vectors encoding shRNA specific to TOP2Β (sh-TOP2Β) or sh-control, deprived of androgen and then treated with DHT (100 nM) or vehicle control for 16 h. GFP positive cells were collected by FACS sorting and subjected to microarray analysis. For inhibitor experiments LNCaP cells were androgen-deprived (control), subsequently stimulated with 100 nM DHT for 16 h (DHT), or pretreated with 100 μM etoposide (DHT+ET) or 100 μM merbarone (DHT+Mer) for 2 h prior to DHT stimulation.
| | Sample_growth_protocol_ch1 = LNCaP cells were propagated in RPMI medium supplemented with 10% fetal bovine serum ( | steady state). In order to deplete cells of basal androgens, all cells were washed with serum-free medium 3 times for 1 h and incubated in 5% charcoal-stripped FBS containing medium for 48 h prior to experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cell lines using a RNeasy RNA extraction kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Samples were hybridized to HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) according to the manufacturer’s protocols at the Johns Hopkins Microarray facility.
| | Sample_scan_protocol | HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) were scanned on the Affymetrix GeneChip Scanner 3000 7G at the Johns Hopkins Microarray facility
| | Sample_data_processing | Data from all microarrays were preprocessed in a single batch using RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Aryee
| | Sample_contact_laboratory | Srinivasan Yegnasubramanian
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University School of Medicine
| | Sample_contact_address | 1650 Orleans St
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484654/suppl/GSM484654.CEL.gz
| | Sample_series_id | GSE19445
| | Sample_data_row_count | 54675
| | |
|
GSM484655 | GPL570 |
|
shrna_series-GFP+DHT
|
LNCaP cells - GFP + DHT
|
cell line: LNCaP
protocol: control transfection and androgen deprivation
agent: DHT
|
sh-control vector transfection and androgen deprivation followed by DHT stimulation for 16 h.
|
| Sample_geo_accession | GSM484655
| | Sample_status | Public on Jul 04 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Jun 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For sh-RNA knockdown experiments LNCaP cells were transfected with GFP expression vectors encoding shRNA specific to TOP2Β (sh-TOP2Β) or sh-control, deprived of androgen and then treated with DHT (100 nM) or vehicle control for 16 h. GFP positive cells were collected by FACS sorting and subjected to microarray analysis. For inhibitor experiments LNCaP cells were androgen-deprived (control), subsequently stimulated with 100 nM DHT for 16 h (DHT), or pretreated with 100 μM etoposide (DHT+ET) or 100 μM merbarone (DHT+Mer) for 2 h prior to DHT stimulation.
| | Sample_growth_protocol_ch1 = LNCaP cells were propagated in RPMI medium supplemented with 10% fetal bovine serum ( | steady state). In order to deplete cells of basal androgens, all cells were washed with serum-free medium 3 times for 1 h and incubated in 5% charcoal-stripped FBS containing medium for 48 h prior to experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cell lines using a RNeasy RNA extraction kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Samples were hybridized to HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) according to the manufacturer’s protocols at the Johns Hopkins Microarray facility.
| | Sample_scan_protocol | HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) were scanned on the Affymetrix GeneChip Scanner 3000 7G at the Johns Hopkins Microarray facility
| | Sample_data_processing | Data from all microarrays were preprocessed in a single batch using RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Aryee
| | Sample_contact_laboratory | Srinivasan Yegnasubramanian
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University School of Medicine
| | Sample_contact_address | 1650 Orleans St
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484655/suppl/GSM484655.CEL.gz
| | Sample_series_id | GSE19445
| | Sample_data_row_count | 54675
| | |
|
GSM484656 | GPL570 |
|
shrna_series-GFP+shtop
|
LNCaP cells - GFP + TOPO2B shRNA
|
cell line: LNCaP
protocol: TOPO2B knockdown and androgen deprivation
|
sh-TOP2B vector transfection and androgen deprivation.
|
| Sample_geo_accession | GSM484656
| | Sample_status | Public on Jul 04 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Jun 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For sh-RNA knockdown experiments LNCaP cells were transfected with GFP expression vectors encoding shRNA specific to TOP2Β (sh-TOP2Β) or sh-control, deprived of androgen and then treated with DHT (100 nM) or vehicle control for 16 h. GFP positive cells were collected by FACS sorting and subjected to microarray analysis. For inhibitor experiments LNCaP cells were androgen-deprived (control), subsequently stimulated with 100 nM DHT for 16 h (DHT), or pretreated with 100 μM etoposide (DHT+ET) or 100 μM merbarone (DHT+Mer) for 2 h prior to DHT stimulation.
| | Sample_growth_protocol_ch1 = LNCaP cells were propagated in RPMI medium supplemented with 10% fetal bovine serum ( | steady state). In order to deplete cells of basal androgens, all cells were washed with serum-free medium 3 times for 1 h and incubated in 5% charcoal-stripped FBS containing medium for 48 h prior to experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cell lines using a RNeasy RNA extraction kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Samples were hybridized to HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) according to the manufacturer’s protocols at the Johns Hopkins Microarray facility.
| | Sample_scan_protocol | HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) were scanned on the Affymetrix GeneChip Scanner 3000 7G at the Johns Hopkins Microarray facility
| | Sample_data_processing | Data from all microarrays were preprocessed in a single batch using RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Aryee
| | Sample_contact_laboratory | Srinivasan Yegnasubramanian
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University School of Medicine
| | Sample_contact_address | 1650 Orleans St
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484656/suppl/GSM484656.CEL.gz
| | Sample_series_id | GSE19445
| | Sample_data_row_count | 54675
| | |
|
GSM484657 | GPL570 |
|
shrna_series-GFP+shtop+DHT
|
LNCaP cells - GFP + DHT + TOPO2B shRNA
|
cell line: LNCaP
protocol: TOPO2B knockdown and androgen deprivation
agent: DHT
|
sh-TOP2B vector transfection and androgen deprivation followed by DHT stimulation for 16 h.
|
| Sample_geo_accession | GSM484657
| | Sample_status | Public on Jul 04 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Jun 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For sh-RNA knockdown experiments LNCaP cells were transfected with GFP expression vectors encoding shRNA specific to TOP2Β (sh-TOP2Β) or sh-control, deprived of androgen and then treated with DHT (100 nM) or vehicle control for 16 h. GFP positive cells were collected by FACS sorting and subjected to microarray analysis. For inhibitor experiments LNCaP cells were androgen-deprived (control), subsequently stimulated with 100 nM DHT for 16 h (DHT), or pretreated with 100 μM etoposide (DHT+ET) or 100 μM merbarone (DHT+Mer) for 2 h prior to DHT stimulation.
| | Sample_growth_protocol_ch1 = LNCaP cells were propagated in RPMI medium supplemented with 10% fetal bovine serum ( | steady state). In order to deplete cells of basal androgens, all cells were washed with serum-free medium 3 times for 1 h and incubated in 5% charcoal-stripped FBS containing medium for 48 h prior to experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cell lines using a RNeasy RNA extraction kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | Samples were hybridized to HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) according to the manufacturer’s protocols at the Johns Hopkins Microarray facility.
| | Sample_scan_protocol | HG-U133 2.0 Plus whole genome gene expression microarrays (Affymetrix) were scanned on the Affymetrix GeneChip Scanner 3000 7G at the Johns Hopkins Microarray facility
| | Sample_data_processing | Data from all microarrays were preprocessed in a single batch using RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Aryee
| | Sample_contact_laboratory | Srinivasan Yegnasubramanian
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University School of Medicine
| | Sample_contact_address | 1650 Orleans St
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484657/suppl/GSM484657.CEL.gz
| | Sample_series_id | GSE19445
| | Sample_data_row_count | 54675
| | |
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