Search results for the GEO ID: GSE15943  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM399983 | GPL339 |
|
01-WT1-3577 (Normal)
|
Normal
|
tissue: prostate
phenotype: Normal
genotype: WT
|
01-WT1-3577
|
| Sample_geo_accession | GSM399983
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399983/suppl/GSM399983.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399984 | GPL339 |
|
02-WT2-3578 (Normal)
|
Normal
|
tissue: prostate
phenotype: Normal
genotype: WT
|
02-WT2-3578
|
| Sample_geo_accession | GSM399984
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399984/suppl/GSM399984.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399985 | GPL339 |
|
03-WT3-3616 (Normal)
|
Normal
|
tissue: prostate
phenotype: Normal
genotype: WT
|
03-WT3-3616
|
| Sample_geo_accession | GSM399985
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399985/suppl/GSM399985.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399986 | GPL339 |
|
04-WT4-6189 (Normal)
|
Normal
|
tissue: prostate
phenotype: Normal
genotype: WT
|
04-WT4-6189
|
| Sample_geo_accession | GSM399986
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399986/suppl/GSM399986.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399987 | GPL339 |
|
05-N1-1421 (Dysplasia-LGPIN)
|
Dysplasia-LGPIN
|
tissue: prostate
phenotype: Dysplasia-LGPIN
genotype: N
|
05-N1-1421
|
| Sample_geo_accession | GSM399987
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399987/suppl/GSM399987.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399988 | GPL339 |
|
06-N2-3442 (Dysplasia-LGPIN)
|
Dysplasia-LGPIN
|
tissue: prostate
phenotype: Dysplasia-LGPIN
genotype: N
|
06-N2-3442
|
| Sample_geo_accession | GSM399988
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399988/suppl/GSM399988.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399989 | GPL339 |
|
07-N3-3459 (Dysplasia-LGPIN)
|
Dysplasia-LGPIN
|
tissue: prostate
phenotype: Dysplasia-LGPIN
genotype: N
|
07-N3-3459
|
| Sample_geo_accession | GSM399989
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399989/suppl/GSM399989.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399990 | GPL339 |
|
08-N4-3583 (Dysplasia-LGPIN)
|
Dysplasia-LGPIN
|
tissue: prostate
phenotype: Dysplasia-LGPIN
genotype: N
|
08-N4-3583
|
| Sample_geo_accession | GSM399990
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399990/suppl/GSM399990.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399991 | GPL339 |
|
09-P1-6108 (HGPIN-Cancer)
|
HGPIN-Cancer
|
tissue: prostate
phenotype: HGPIN-Cancer
genotype: P
|
09-P1-6108
|
| Sample_geo_accession | GSM399991
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399991/suppl/GSM399991.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399992 | GPL339 |
|
10-P2-6245 (HGPIN-Cancer)
|
HGPIN-Cancer
|
tissue: prostate
phenotype: HGPIN-Cancer
genotype: P
|
10-P2-6245
|
| Sample_geo_accession | GSM399992
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399992/suppl/GSM399992.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399993 | GPL339 |
|
11-P3-6934 (Dysplasia-LGPIN)
|
Dysplasia-LGPIN
|
tissue: prostate
phenotype: Dysplasia-LGPIN
genotype: P
|
11-P3-6934
|
| Sample_geo_accession | GSM399993
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399993/suppl/GSM399993.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399994 | GPL339 |
|
12-NP1-5472 (HGPIN-Cancer)
|
HGPIN-Cancer
|
tissue: prostate
phenotype: HGPIN-Cancer
genotype: NP
|
12-NP1-5472
|
| Sample_geo_accession | GSM399994
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399994/suppl/GSM399994.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399995 | GPL339 |
|
13-NP2-6490 (HGPIN-Cancer)
|
HGPIN-Cancer
|
tissue: prostate
phenotype: HGPIN-Cancer
genotype: NP
|
13-NP2-6490
|
| Sample_geo_accession | GSM399995
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399995/suppl/GSM399995.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399996 | GPL339 |
|
14-NP3-8184 (Dysplasia-LGPIN)
|
Dysplasia-LGPIN
|
tissue: prostate
phenotype: Dysplasia-LGPIN
genotype: NP
|
14-NP3-8184
|
| Sample_geo_accession | GSM399996
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399996/suppl/GSM399996.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399997 | GPL339 |
|
15-NP4-8396 (Dysplasia-LGPIN)
|
Dysplasia-LGPIN
|
tissue: prostate
phenotype: Dysplasia-LGPIN
genotype: NP
|
15-NP4-8396
|
| Sample_geo_accession | GSM399997
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399997/suppl/GSM399997.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399998 | GPL339 |
|
16-NP5-8643 (HGPIN-Cancer)
|
HGPIN-Cancer
|
tissue: prostate
phenotype: HGPIN-Cancer
genotype: NP
|
16-NP5-8643
|
| Sample_geo_accession | GSM399998
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399998/suppl/GSM399998.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM399999 | GPL339 |
|
17-TH2-8054 (HGPIN-Cancer)
|
HGPIN-Cancer
|
tissue: prostate
phenotype: HGPIN-Cancer
genotype: TH
|
17-TH2-8054
|
| Sample_geo_accession | GSM399999
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM399nnn/GSM399999/suppl/GSM399999.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM400000 | GPL339 |
|
18-TH4-8361 (Dysplasia-LGPIN)
|
Dysplasia-LGPIN
|
tissue: prostate
phenotype: Dysplasia-LGPIN
genotype: TH
|
18-TH4-8361
|
| Sample_geo_accession | GSM400000
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400000/suppl/GSM400000.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM400001 | GPL339 |
|
19-AI-NP1-4901 (AI-HGPIN)
|
AI-HGPIN
|
tissue: prostate
phenotype: AI-HGPIN
genotype: NP
|
19-AI-NP1-4901
|
| Sample_geo_accession | GSM400001
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400001/suppl/GSM400001.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM400002 | GPL339 |
|
20-AI-P1-4903 (AI-HGPIN)
|
AI-HGPIN
|
tissue: prostate
phenotype: AI-HGPIN
genotype: P
|
20-AI-P1-4903
|
| Sample_geo_accession | GSM400002
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400002/suppl/GSM400002.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM400003 | GPL339 |
|
21-AI-NP2-4904 (AI-HGPIN)
|
AI-HGPIN
|
tissue: prostate
phenotype: AI-HGPIN
genotype: NP
|
21-AI-NP2-4904
|
| Sample_geo_accession | GSM400003
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400003/suppl/GSM400003.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM400004 | GPL339 |
|
22-AI-P2-4905 (AI-HGPIN)
|
AI-HGPIN
|
tissue: prostate
phenotype: AI-HGPIN
genotype: P
|
22-AI-P2-4905
|
| Sample_geo_accession | GSM400004
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400004/suppl/GSM400004.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM400005 | GPL339 |
|
23-AI-NP3-3584 (AI-Cancer-MET)
|
AI-Cancer-MET
|
tissue: prostate
phenotype: AI-Cancer-MET
genotype: NP
|
23-AI-NP3-3584
|
| Sample_geo_accession | GSM400005
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400005/suppl/GSM400005.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM400006 | GPL339 |
|
24-AI-NP4-4522 (AI-Cancer-MET)
|
AI-Cancer-MET
|
tissue: prostate
phenotype: AI-Cancer-MET
genotype: NP
|
24-AI-NP4-4522
|
| Sample_geo_accession | GSM400006
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400006/suppl/GSM400006.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM400007 | GPL339 |
|
25-AI-NP5-4896 (AI-Cancer-MET)
|
AI-Cancer-MET
|
tissue: prostate
phenotype: AI-Cancer-MET
genotype: NP
|
25-AI-NP5-4896
|
| Sample_geo_accession | GSM400007
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400007/suppl/GSM400007.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
GSM400008 | GPL339 |
|
26-AI-NP6-5338 (AI-Cancer-MET)
|
AI-Cancer-MET
|
tissue: prostate
phenotype: AI-Cancer-MET
genotype: NP
|
26-AI-NP6-5338
|
| Sample_geo_accession | GSM400008
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | May 04 2009
| | Sample_last_update_date | May 04 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of cRNA was carried out using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific). Twenty µg of biotinilated RNA probe was fragmented and hybridized to MOE430A GeneChips (Affymetrix).
| | Sample_hyb_protocol | Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
| | Sample_scan_protocol | GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
| | Sample_data_processing | Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM400nnn/GSM400008/suppl/GSM400008.CEL.gz
| | Sample_series_id | GSE15943
| | Sample_data_row_count | 22690
| | |
|
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