Search results for the GEO ID: GSE14988  |
(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 |
GSM374150 | GPL570 |
|
control, biological rep1
|
LNCaP
|
cell line: LNCaP
cell type: cancer cell culture
|
control, biological rep1
|
| Sample_geo_accession | GSM374150
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 25 2009
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP cells were maintained for three days before stimulation with 100 nM dihydrotestosterone (DHT) for 48 hours
| | Sample_growth_protocol_ch1 | LNCaP cells were maintained in phenol red-free RPMI supplemented with 10% charcoal/dextran
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM374nnn/GSM374150/suppl/GSM374150.CEL.gz
| | Sample_series_id | GSE14988
| | Sample_series_id | GSE14990
| | Sample_data_row_count | 54675
| | |
|
GSM374151 | GPL570 |
|
control, biological rep2
|
LNCaP
|
cell line: LNCaP
cell type: cancer cell culture
|
control, biological rep2
|
| Sample_geo_accession | GSM374151
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 25 2009
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP cells were maintained for three days before stimulation with 100 nM dihydrotestosterone (DHT) for 48 hours
| | Sample_growth_protocol_ch1 | LNCaP cells were maintained in phenol red-free RPMI supplemented with 10% charcoal/dextran
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM374nnn/GSM374151/suppl/GSM374151.CEL.gz
| | Sample_series_id | GSE14988
| | Sample_series_id | GSE14990
| | Sample_data_row_count | 54675
| | |
|
GSM374152 | GPL570 |
|
control, biological rep3
|
LNCaP
|
cell line: LNCaP
cell type: cancer cell culture
|
control, biological rep3
|
| Sample_geo_accession | GSM374152
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 25 2009
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP cells were maintained for three days before stimulation with 100 nM dihydrotestosterone (DHT) for 48 hours
| | Sample_growth_protocol_ch1 | LNCaP cells were maintained in phenol red-free RPMI supplemented with 10% charcoal/dextran
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM374nnn/GSM374152/suppl/GSM374152.CEL.gz
| | Sample_series_id | GSE14988
| | Sample_series_id | GSE14990
| | Sample_data_row_count | 54675
| | |
|
GSM374153 | GPL570 |
|
DHT stimulation, biological rep1
|
LNCaP
|
cell line: LNCaP
cell type: cancer cell culture
|
DHT stimulation, biological rep1
|
| Sample_geo_accession | GSM374153
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 25 2009
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP cells were maintained for three days before stimulation with 100 nM dihydrotestosterone (DHT) for 48 hours
| | Sample_growth_protocol_ch1 | LNCaP cells were maintained in phenol red-free RPMI supplemented with 10% charcoal/dextran
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM374nnn/GSM374153/suppl/GSM374153.CEL.gz
| | Sample_series_id | GSE14988
| | Sample_series_id | GSE14990
| | Sample_data_row_count | 54675
| | |
|
GSM374154 | GPL570 |
|
DHT stimulation, biological rep2
|
LNCaP
|
cell line: LNCaP
cell type: cancer cell culture
|
DHT stimulation, biological rep2
|
| Sample_geo_accession | GSM374154
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 25 2009
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP cells were maintained for three days before stimulation with 100 nM dihydrotestosterone (DHT) for 48 hours
| | Sample_growth_protocol_ch1 | LNCaP cells were maintained in phenol red-free RPMI supplemented with 10% charcoal/dextran
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM374nnn/GSM374154/suppl/GSM374154.CEL.gz
| | Sample_series_id | GSE14988
| | Sample_series_id | GSE14990
| | Sample_data_row_count | 54675
| | |
|
GSM374155 | GPL570 |
|
DHT stimulation, biological rep3
|
LNCaP
|
cell line: LNCaP
cell type: cancer cell culture
|
DHT stimulation, biological rep3
|
| Sample_geo_accession | GSM374155
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Feb 25 2009
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP cells were maintained for three days before stimulation with 100 nM dihydrotestosterone (DHT) for 48 hours
| | Sample_growth_protocol_ch1 | LNCaP cells were maintained in phenol red-free RPMI supplemented with 10% charcoal/dextran
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | QIAGEN RNeasy protocol and reagents for extraction of total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ben,S.,Wittner
| | Sample_contact_email | wittner.ben@mgh.harvard.edu
| | Sample_contact_laboratory | Ramaswamy
| | Sample_contact_department | Center for Cancer Research
| | Sample_contact_institute | Massachusetts General Hospital
| | Sample_contact_address | 185 Cambridge St.
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01945
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM374nnn/GSM374155/suppl/GSM374155.CEL.gz
| | Sample_series_id | GSE14988
| | Sample_series_id | GSE14990
| | 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: |
|
|
|
Select expression type |
| Transcripts profile based on; |
A. Differential status (Up/Down regulation) |
|
|
Regulation type |
|
Fold change |
|
p-value |
|
|
|
B. Absolute calls (Transcribed/Not-detected) |
|
|
| Derive calls within/across groups |
Within groups |
|
|
Detection status |
|
Percentage detection |
|
|
Across groups |
|
|
Detection status |
First group: |
- |
Second group:
|
Percentage detection |
First group: |
- |
Second group:
|
|
|
| |
Filter results by number of probes |
|
|
