Search results for the GEO ID: GSE17466  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM435790 | GPL570 |
|
EV-1
|
iPrEC cell line transfected with the empty vector, sample: EV-1
|
type: Cell culture
cell line: iPrEC
disease state: Transfection control
|
No additional description available for sample: EV-1
|
| Sample_geo_accession | GSM435790
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435790/suppl/GSM435790.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435791 | GPL570 |
|
CP_EV1
|
iPrEC cell line transfected with the empty vector, sample: CP_EV1
|
type: Cell culture
cell line: iPrEC
disease state: Transfection control
|
No additional description available for sample: CP_EV1
|
| Sample_geo_accession | GSM435791
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435791/suppl/GSM435791.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435792 | GPL570 |
|
CP_EV2
|
iPrEC cell line transfected with the empty vector, sample: CP_EV2
|
type: Cell culture
cell line: iPrEC
disease state: Transfection control
|
No additional description available for sample: CP_EV2
|
| Sample_geo_accession | GSM435792
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435792/suppl/GSM435792.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435793 | GPL570 |
|
CP_WT1
|
iPrEC cell line transfected with the wild-type USP2A, sample: CP_WT1
|
type: Cell culture
cell line: iPrEC
disease state: Expression of wild-type USP2A
|
No additional description available for sample: CP_WT1
|
| Sample_geo_accession | GSM435793
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435793/suppl/GSM435793.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435794 | GPL570 |
|
CP_WT2
|
iPrEC cell line transfected with the wild-type USP2A, sample: CP_WT2
|
type: Cell culture
cell line: iPrEC
disease state: Expression of wild-type USP2A
|
No additional description available for sample: CP_WT2
|
| Sample_geo_accession | GSM435794
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435794/suppl/GSM435794.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435795 | GPL570 |
|
CP_Mut1
|
iPrEC cell line transfected with the mutant USP2A, sample: CP_Mut1
|
type: Cell culture
cell line: iPrEC
disease state: Expression of mutant USP2A
|
No additional description available for sample: CP_Mut1
|
| Sample_geo_accession | GSM435795
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435795/suppl/GSM435795.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435796 | GPL570 |
|
CP_Mut2
|
iPrEC cell line transfected with the mutant USP2A, sample: CP_Mut2
|
type: Cell culture
cell line: iPrEC
disease state: Expression of mutant USP2A
|
No additional description available for sample: CP_Mut2
|
| Sample_geo_accession | GSM435796
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435796/suppl/GSM435796.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435797 | GPL570 |
|
Mut-1
|
iPrEC cell line transfected with the mutant USP2A, sample: Mut-1
|
type: Cell culture
cell line: iPrEC
disease state: Expression of mutant USP2A
|
No additional description available for sample: Mut-1
|
| Sample_geo_accession | GSM435797
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435797/suppl/GSM435797.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435798 | GPL570 |
|
WT-1
|
iPrEC cell line transfected with the wild-type USP2A, sample: WT-1
|
type: Cell culture
cell line: iPrEC
disease state: Expression of wild-type USP2A
|
No additional description available for sample: WT-1
|
| Sample_geo_accession | GSM435798
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435798/suppl/GSM435798.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435799 | GPL570 |
|
EV-2
|
iPrEC cell line transfected with the empty vector, sample: EV-2
|
type: Cell culture
cell line: iPrEC
disease state: Transfection control
|
No additional description available for sample: EV-2
|
| Sample_geo_accession | GSM435799
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435799/suppl/GSM435799.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435800 | GPL570 |
|
Mut-2
|
iPrEC cell line transfected with the mutant USP2A, sample: Mut-2
|
type: Cell culture
cell line: iPrEC
disease state: Expression of mutant USP2A
|
No additional description available for sample: Mut-2
|
| Sample_geo_accession | GSM435800
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435800/suppl/GSM435800.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435801 | GPL570 |
|
WT-2
|
iPrEC cell line transfected with the wild-type USP2A, sample: WT-2
|
type: Cell culture
cell line: iPrEC
disease state: Expression of wild-type USP2A
|
No additional description available for sample: WT-2
|
| Sample_geo_accession | GSM435801
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435801/suppl/GSM435801.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435802 | GPL570 |
|
EV-3
|
iPrEC cell line transfected with the empty vector, sample: EV-3
|
type: Cell culture
cell line: iPrEC
disease state: Transfection control
|
No additional description available for sample: EV-3
|
| Sample_geo_accession | GSM435802
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435802/suppl/GSM435802.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435803 | GPL570 |
|
Mut-3
|
iPrEC cell line transfected with the mutant USP2A, sample: Mut-3
|
type: Cell culture
cell line: iPrEC
disease state: Expression of mutant USP2A
|
No additional description available for sample: Mut-3
|
| Sample_geo_accession | GSM435803
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435803/suppl/GSM435803.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
|
GSM435804 | GPL570 |
|
WT-3
|
iPrEC cell line transfected with the wild-type USP2A, sample: WT-3
|
type: Cell culture
cell line: iPrEC
disease state: Expression of wild-type USP2A
|
No additional description available for sample: WT-3
|
| Sample_geo_accession | GSM435804
| | Sample_status | Public on Dec 27 2011
| | Sample_submission_date | Jul 31 2009
| | Sample_last_update_date | Dec 27 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA, and then transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.
| | Sample_hyb_protocol | Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).
| | Sample_scan_protocol | The gene chip was scanned using a confocal laser scanner (Affymetrix).
| | Sample_data_processing | The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luigi,,Marchionni
| | Sample_contact_email | marchion@jhu.edu
| | Sample_contact_phone | 410-502-8179
| | Sample_contact_fax | 410-502-5742
| | Sample_contact_laboratory | Cancer Biology Program
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Johns Hopkins University
| | Sample_contact_address | 1550 Orleans St., CRB2, Room 1M52
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://luigimarchionni.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435804/suppl/GSM435804.CEL.gz
| | Sample_series_id | GSE17466
| | Sample_data_row_count | 54675
| | |
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