Search results for the GEO ID: GSE14088 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM353503 | GPL1261 |
|
control shRNA, biological replicate 1
|
NIH 3T3 cells
|
NIH 3T3 transduced with control retroviral shRNA vector
|
Gene expression data from NIH 3T3 cells transduced with vector containing control shRNA.
|
Sample_geo_accession | GSM353503
| Sample_status | Public on Mar 24 2009
| Sample_submission_date | Dec 22 2008
| Sample_last_update_date | Mar 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were transduced with an shRNA retroviral vector and harvested 5 days later for RNA isolation.
| Sample_growth_protocol_ch1 | NIH 3T3 cells expressing Ube2f were grown (37C, %% CO2) in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum (Hyclone), 4mM glutamine, and 100 units each of penicillin and streptomycin (Life Technologies).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on mouse GeneChip 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| Sample_data_processing | The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Geoffrey,,Neale
| Sample_contact_email | geoffrey.neale@stjude.org
| Sample_contact_institute | St Jude Childrens Research Hospital
| Sample_contact_address | 332 N Lauderdale St
| Sample_contact_city | Memphis
| Sample_contact_state | TN
| Sample_contact_zip/postal_code | 38105
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM353nnn/GSM353503/suppl/GSM353503.CEL.gz
| Sample_series_id | GSE14088
| Sample_data_row_count | 45101
| |
|
GSM353504 | GPL1261 |
|
control shRNA, biological replicate 2
|
NIH 3T3 cells
|
NIH 3T3 transduced with control retroviral shRNA vector
|
Gene expression data from NIH 3T3 cells transduced with vector containing control shRNA.
|
Sample_geo_accession | GSM353504
| Sample_status | Public on Mar 24 2009
| Sample_submission_date | Dec 22 2008
| Sample_last_update_date | Mar 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were transduced with an shRNA retroviral vector and harvested 5 days later for RNA isolation.
| Sample_growth_protocol_ch1 | NIH 3T3 cells expressing Ube2f were grown (37C, %% CO2) in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum (Hyclone), 4mM glutamine, and 100 units each of penicillin and streptomycin (Life Technologies).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on mouse GeneChip 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| Sample_data_processing | The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Geoffrey,,Neale
| Sample_contact_email | geoffrey.neale@stjude.org
| Sample_contact_institute | St Jude Childrens Research Hospital
| Sample_contact_address | 332 N Lauderdale St
| Sample_contact_city | Memphis
| Sample_contact_state | TN
| Sample_contact_zip/postal_code | 38105
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM353nnn/GSM353504/suppl/GSM353504.CEL.gz
| Sample_series_id | GSE14088
| Sample_data_row_count | 45101
| |
|
GSM353505 | GPL1261 |
|
Ube2m shRNA, biological replicate 1
|
NIH 3T3 cells
|
NIH 3T3 transduced with retroviral shRNA vector targeting Ube2m
|
Gene expression data from NIH 3T3 cells transduced with shRNA vector targeting Ube2m.
|
Sample_geo_accession | GSM353505
| Sample_status | Public on Mar 24 2009
| Sample_submission_date | Dec 22 2008
| Sample_last_update_date | Mar 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were transduced with an shRNA retroviral vector and harvested 5 days later for RNA isolation.
| Sample_growth_protocol_ch1 | NIH 3T3 cells expressing Ube2f were grown (37C, %% CO2) in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum (Hyclone), 4mM glutamine, and 100 units each of penicillin and streptomycin (Life Technologies).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on mouse GeneChip 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| Sample_data_processing | The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Geoffrey,,Neale
| Sample_contact_email | geoffrey.neale@stjude.org
| Sample_contact_institute | St Jude Childrens Research Hospital
| Sample_contact_address | 332 N Lauderdale St
| Sample_contact_city | Memphis
| Sample_contact_state | TN
| Sample_contact_zip/postal_code | 38105
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM353nnn/GSM353505/suppl/GSM353505.CEL.gz
| Sample_series_id | GSE14088
| Sample_data_row_count | 45101
| |
|
GSM353506 | GPL1261 |
|
Ube2m shRNA, biological replicate 2
|
NIH 3T3 cells
|
NIH 3T3 transduced with retroviral shRNA vector targeting Ube2m
|
Gene expression data from NIH 3T3 cells transduced with shRNA vector targeting Ube2m.
|
Sample_geo_accession | GSM353506
| Sample_status | Public on Mar 24 2009
| Sample_submission_date | Dec 22 2008
| Sample_last_update_date | Mar 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were transduced with an shRNA retroviral vector and harvested 5 days later for RNA isolation.
| Sample_growth_protocol_ch1 | NIH 3T3 cells expressing Ube2f were grown (37C, %% CO2) in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum (Hyclone), 4mM glutamine, and 100 units each of penicillin and streptomycin (Life Technologies).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on mouse GeneChip 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| Sample_data_processing | The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Geoffrey,,Neale
| Sample_contact_email | geoffrey.neale@stjude.org
| Sample_contact_institute | St Jude Childrens Research Hospital
| Sample_contact_address | 332 N Lauderdale St
| Sample_contact_city | Memphis
| Sample_contact_state | TN
| Sample_contact_zip/postal_code | 38105
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM353nnn/GSM353506/suppl/GSM353506.CEL.gz
| Sample_series_id | GSE14088
| Sample_data_row_count | 45101
| |
|
GSM353507 | GPL1261 |
|
Ube2f shRNA, biological replicate 1
|
NIH 3T3 cells
|
NIH 3T3 transduced with retroviral shRNA vector targeting Ube2f
|
Gene expression data from NIH 3T3 cells transduced with shRNA vector targeting Ube2f.
|
Sample_geo_accession | GSM353507
| Sample_status | Public on Mar 24 2009
| Sample_submission_date | Dec 22 2008
| Sample_last_update_date | Mar 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were transduced with an shRNA retroviral vector and harvested 5 days later for RNA isolation.
| Sample_growth_protocol_ch1 | NIH 3T3 cells expressing Ube2f were grown (37C, %% CO2) in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum (Hyclone), 4mM glutamine, and 100 units each of penicillin and streptomycin (Life Technologies).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on mouse GeneChip 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| Sample_data_processing | The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Geoffrey,,Neale
| Sample_contact_email | geoffrey.neale@stjude.org
| Sample_contact_institute | St Jude Childrens Research Hospital
| Sample_contact_address | 332 N Lauderdale St
| Sample_contact_city | Memphis
| Sample_contact_state | TN
| Sample_contact_zip/postal_code | 38105
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM353nnn/GSM353507/suppl/GSM353507.CEL.gz
| Sample_series_id | GSE14088
| Sample_data_row_count | 45101
| |
|
GSM353508 | GPL1261 |
|
Ube2f shRNA, biological replicate 2
|
NIH 3T3 cells
|
NIH 3T3 transduced with retroviral shRNA vector targeting Ube2f
|
Gene expression data from NIH 3T3 cells transduced with shRNA vector targeting Ube2f.
|
Sample_geo_accession | GSM353508
| Sample_status | Public on Mar 24 2009
| Sample_submission_date | Dec 22 2008
| Sample_last_update_date | Mar 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were transduced with an shRNA retroviral vector and harvested 5 days later for RNA isolation.
| Sample_growth_protocol_ch1 | NIH 3T3 cells expressing Ube2f were grown (37C, %% CO2) in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum (Hyclone), 4mM glutamine, and 100 units each of penicillin and streptomycin (Life Technologies).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on mouse GeneChip 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| Sample_data_processing | The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Geoffrey,,Neale
| Sample_contact_email | geoffrey.neale@stjude.org
| Sample_contact_institute | St Jude Childrens Research Hospital
| Sample_contact_address | 332 N Lauderdale St
| Sample_contact_city | Memphis
| Sample_contact_state | TN
| Sample_contact_zip/postal_code | 38105
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM353nnn/GSM353508/suppl/GSM353508.CEL.gz
| Sample_series_id | GSE14088
| Sample_data_row_count | 45101
| |
|
GSM353509 | GPL1261 |
|
control shRNA, biological replicate 3
|
NIH 3T3 cells
|
NIH 3T3 transduced with control retroviral shRNA vector
|
Gene expression data from NIH 3T3 cells transduced with vector containing control shRNA.
|
Sample_geo_accession | GSM353509
| Sample_status | Public on Mar 24 2009
| Sample_submission_date | Dec 22 2008
| Sample_last_update_date | Mar 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were transduced with an shRNA retroviral vector and harvested 5 days later for RNA isolation.
| Sample_growth_protocol_ch1 | NIH 3T3 cells expressing Ube2f were grown (37C, %% CO2) in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum (Hyclone), 4mM glutamine, and 100 units each of penicillin and streptomycin (Life Technologies).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on mouse GeneChip 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| Sample_data_processing | The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Geoffrey,,Neale
| Sample_contact_email | geoffrey.neale@stjude.org
| Sample_contact_institute | St Jude Childrens Research Hospital
| Sample_contact_address | 332 N Lauderdale St
| Sample_contact_city | Memphis
| Sample_contact_state | TN
| Sample_contact_zip/postal_code | 38105
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM353nnn/GSM353509/suppl/GSM353509.CEL.gz
| Sample_series_id | GSE14088
| Sample_data_row_count | 45101
| |
|
GSM353510 | GPL1261 |
|
Ube2m shRNA, biological replicate 3
|
NIH 3T3 cells
|
NIH 3T3 transduced with retroviral shRNA vector targeting Ube2m
|
Gene expression data from NIH 3T3 cells transduced with shRNA vector targeting Ube2m.
|
Sample_geo_accession | GSM353510
| Sample_status | Public on Mar 24 2009
| Sample_submission_date | Dec 22 2008
| Sample_last_update_date | Mar 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were transduced with an shRNA retroviral vector and harvested 5 days later for RNA isolation.
| Sample_growth_protocol_ch1 | NIH 3T3 cells expressing Ube2f were grown (37C, %% CO2) in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum (Hyclone), 4mM glutamine, and 100 units each of penicillin and streptomycin (Life Technologies).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on mouse GeneChip 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| Sample_data_processing | The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Geoffrey,,Neale
| Sample_contact_email | geoffrey.neale@stjude.org
| Sample_contact_institute | St Jude Childrens Research Hospital
| Sample_contact_address | 332 N Lauderdale St
| Sample_contact_city | Memphis
| Sample_contact_state | TN
| Sample_contact_zip/postal_code | 38105
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM353nnn/GSM353510/suppl/GSM353510.CEL.gz
| Sample_series_id | GSE14088
| Sample_data_row_count | 45101
| |
|
GSM353511 | GPL1261 |
|
Ube2f shRNA, biological replicate 3
|
NIH 3T3 cells
|
NIH 3T3 transduced with retroviral shRNA vector targeting Ube2f
|
Gene expression data from NIH 3T3 cells transduced with shRNA vector targeting Ube2f.
|
Sample_geo_accession | GSM353511
| Sample_status | Public on Mar 24 2009
| Sample_submission_date | Dec 22 2008
| Sample_last_update_date | Mar 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Cells were transduced with an shRNA retroviral vector and harvested 5 days later for RNA isolation.
| Sample_growth_protocol_ch1 | NIH 3T3 cells expressing Ube2f were grown (37C, %% CO2) in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum (Hyclone), 4mM glutamine, and 100 units each of penicillin and streptomycin (Life Technologies).
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on mouse GeneChip 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| Sample_data_processing | The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| Sample_platform_id | GPL1261
| Sample_contact_name | Geoffrey,,Neale
| Sample_contact_email | geoffrey.neale@stjude.org
| Sample_contact_institute | St Jude Childrens Research Hospital
| Sample_contact_address | 332 N Lauderdale St
| Sample_contact_city | Memphis
| Sample_contact_state | TN
| Sample_contact_zip/postal_code | 38105
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM353nnn/GSM353511/suppl/GSM353511.CEL.gz
| Sample_series_id | GSE14088
| Sample_data_row_count | 45101
| |
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