Search results for the GEO ID: GSE17482  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM435992 | GPL570 |
|
DU145_ctrl#1
|
DU145 cells, control
|
cell line: DU145
cell type: prostrate cancer
|
Gene expression data from DU145 cells transfected with scramble siRNA(control)
|
| Sample_geo_accession | GSM435992
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435992/suppl/GSM435992.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_series_id | GSE17483
| | Sample_data_row_count | 54675
| | |
|
GSM435993 | GPL570 |
|
DU145_ctrl#2
|
DU145 cells, control
|
cell line: DU145
cell type: prostrate cancer
|
Gene expression data from DU145 cells transfected with scramble siRNA(control)
|
| Sample_geo_accession | GSM435993
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435993/suppl/GSM435993.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_series_id | GSE17483
| | Sample_data_row_count | 54675
| | |
|
GSM435994 | GPL570 |
|
DU145_ctrl#3
|
DU145 cells, control
|
cell line: DU145
cell type: prostrate cancer
|
Gene expression data from DU145 cells transfected with scramble siRNA(control)
|
| Sample_geo_accession | GSM435994
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435994/suppl/GSM435994.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_series_id | GSE17483
| | Sample_data_row_count | 54675
| | |
|
GSM435995 | GPL570 |
|
DU145_Stat3#1
|
DU145 cells, Stat3 down-regulated
|
cell line: DU145
cell type: prostrate cancer
|
Gene expression data from DU145 cells transfected with Stat3 siRNA
|
| Sample_geo_accession | GSM435995
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435995/suppl/GSM435995.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_data_row_count | 54675
| | |
|
GSM435996 | GPL570 |
|
DU145_Stat3#2
|
DU145 cells, Stat3 down-regulated
|
cell line: DU145
cell type: prostrate cancer
|
Gene expression data from DU145 cells transfected with Stat3 siRNA
|
| Sample_geo_accession | GSM435996
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435996/suppl/GSM435996.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_data_row_count | 54675
| | |
|
GSM435997 | GPL570 |
|
DU145_Stat3#3
|
DU145 cells, Stat3 down-regulated
|
cell line: DU145
cell type: prostrate cancer
|
Gene expression data from DU145 cells transfected with Stat3 siRNA
|
| Sample_geo_accession | GSM435997
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435997/suppl/GSM435997.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_data_row_count | 54675
| | |
|
GSM435998 | GPL570 |
|
DU145_Stat5a/b#1
|
DU145 cells, Stat5a/b down-regulated
|
cell line: DU145
cell type: prostrate cancer
|
Gene expression data from DU145 cells transfected with Stat5a/b siRNA
|
| Sample_geo_accession | GSM435998
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435998/suppl/GSM435998.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_series_id | GSE17483
| | Sample_data_row_count | 54675
| | |
|
GSM435999 | GPL570 |
|
DU145_Stat5a/b#2
|
DU145 cells, Stat5a/b down-regulated
|
cell line: DU145
cell type: prostrate cancer
|
Gene expression data from DU145 cells transfected with Stat5a/b siRNA
|
| Sample_geo_accession | GSM435999
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435999/suppl/GSM435999.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_series_id | GSE17483
| | Sample_data_row_count | 54675
| | |
|
GSM436000 | GPL570 |
|
DU145_Stat5a/b#3
|
DU145 cells, Stat5a/b down-regulated
|
cell line: DU145
cell type: prostrate cancer
|
Gene expression data from DU145 cells transfected with Stat5a/b siRNA
|
| Sample_geo_accession | GSM436000
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM436nnn/GSM436000/suppl/GSM436000.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_series_id | GSE17483
| | Sample_data_row_count | 54675
| | |
|
GSM436001 | GPL570 |
|
CWR_ctrl#1
|
CWR22Rv1 cells, control
|
cell line: CWR22Rv1
cell type: prostrate cancer
|
Gene expression data from CWR22Rv1 cells transfected with scramble siRNA(control)
|
| Sample_geo_accession | GSM436001
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM436nnn/GSM436001/suppl/GSM436001.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_data_row_count | 54675
| | |
|
GSM436002 | GPL570 |
|
CWR_ctrl#2
|
CWR22Rv1 cells, control
|
cell line: CWR22Rv1
cell type: prostrate cancer
|
Gene expression data from CWR22Rv1 cells transfected with scramble siRNA(control)
|
| Sample_geo_accession | GSM436002
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM436nnn/GSM436002/suppl/GSM436002.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_data_row_count | 54675
| | |
|
GSM436003 | GPL570 |
|
CWR_ctrl#3
|
CWR22Rv1 cells, control
|
cell line: CWR22Rv1
cell type: prostrate cancer
|
Gene expression data from CWR22Rv1 cells transfected with scramble siRNA(control)
|
| Sample_geo_accession | GSM436003
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM436nnn/GSM436003/suppl/GSM436003.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_data_row_count | 54675
| | |
|
GSM436004 | GPL570 |
|
CWR_Stat3#1
|
CWR22Rv1 cells, Stat3 down-regulated
|
cell line: CWR22Rv1
cell type: prostrate cancer
|
Gene expression data from CWR22Rv1 cells transfected with Stat3 siRNA
|
| Sample_geo_accession | GSM436004
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM436nnn/GSM436004/suppl/GSM436004.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_data_row_count | 54675
| | |
|
GSM436005 | GPL570 |
|
CWR_Stat3#2
|
CWR22Rv1 cells, Stat3 down-regulated
|
cell line: CWR22Rv1
cell type: prostrate cancer
|
Gene expression data from CWR22Rv1 cells transfected with Stat3 siRNA
|
| Sample_geo_accession | GSM436005
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM436nnn/GSM436005/suppl/GSM436005.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_data_row_count | 54675
| | |
|
GSM436006 | GPL570 |
|
CWR_Stat3#3
|
CWR22Rv1 cells, Stat3 down-regulated
|
cell line: CWR22Rv1
cell type: prostrate cancer
|
Gene expression data from CWR22Rv1 cells transfected with Stat3 siRNA
|
| Sample_geo_accession | GSM436006
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM436nnn/GSM436006/suppl/GSM436006.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_data_row_count | 54675
| | |
|
GSM436007 | GPL570 |
|
CWR_Stat5a/b#1
|
CWR22Rv1 cells, Stat5a/b down-regulated
|
cell line: CWR22Rv1
cell type: prostrate cancer
|
Gene expression data from CWR22Rv1 cells transfected with Stat5a/b siRNA
|
| Sample_geo_accession | GSM436007
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM436nnn/GSM436007/suppl/GSM436007.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_data_row_count | 54675
| | |
|
GSM436008 | GPL570 |
|
CWR_Stat5a/b#2
|
CWR22Rv1 cells, Stat5a/b down-regulated
|
cell line: CWR22Rv1
cell type: prostrate cancer
|
Gene expression data from CWR22Rv1 cells transfected with Stat5a/b siRNA
|
| Sample_geo_accession | GSM436008
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM436nnn/GSM436008/suppl/GSM436008.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_data_row_count | 54675
| | |
|
GSM436009 | GPL570 |
|
CWR_Stat5a/b#3
|
CWR22Rv1 cells, Stat5a/b down-regulated
|
cell line: CWR22Rv1
cell type: prostrate cancer
|
Gene expression data from CWR22Rv1 cells transfected with Stat5a/b siRNA
|
| Sample_geo_accession | GSM436009
| | Sample_status | Public on Apr 30 2010
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
| | Sample_growth_protocol_ch1 | DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
| | Sample_data_processing | The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marja,,Nevalainen
| | Sample_contact_email | Marja.Nevalainen@jefferson.edu
| | Sample_contact_phone | 215-503-9250
| | Sample_contact_fax | 215-503-9245
| | Sample_contact_laboratory | Nevalainen
| | Sample_contact_department | Cancer Biology
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 S. 10th St
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19107
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM436nnn/GSM436009/suppl/GSM436009.CEL.gz
| | Sample_series_id | GSE17482
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
