Search results for the GEO ID: GSE17300  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM432926 | GPL570 |
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USF1 replicate 1
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HEK293T cell line
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cell line: HEK293T
|
n/a
|
| Sample_geo_accession | GSM432926
| | Sample_status | Public on Sep 14 2009
| | Sample_submission_date | Jul 24 2009
| | Sample_last_update_date | Sep 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was collected using the RNeasy Plus Mini Kit (Cat No. 74134) 48 hours after transient transfection of HEK293T cells.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were then converted to cRNA probes using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).
| | Sample_hyb_protocol | The cRNA probes were then hybridized using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).
| | Sample_scan_protocol | The chips were scanned using the GeneArray scanner (Affymetrix) to produce CEL files.
| | Sample_data_processing | A rigorous quality control pipeline was developed to prepare the gene expression microarray data for analysis. First, the CEL files were imported into R 2.8.0 using the justRMA function of the Affymetrix library from Bioconductor, which applies background subtraction and quantile normalization. An alternate CDF file (U133Plus2msk.cdf.gz) was used to exclude mis-targeted and nonspecific probes from the microarrays (Zhang et al. 2005), and probesets with less than 7 remaining probes were also excluded. Probesets with more than 50% absent calls were excluded, as calculated using the panp package from Bioconductor. Finally, the ComBat library in R was used to correct for batch effect (Johnson et al. 2007).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Christopher,L,Plaisier
| | Sample_contact_email | plaisier@ucla.edu
| | Sample_contact_phone | 310 794-9802
| | Sample_contact_fax | 310 794-5446
| | Sample_contact_laboratory | Paivi Pajukanta
| | Sample_contact_department | Human Genetics
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 695 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095-7088
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432926/suppl/GSM432926.CEL.gz
| | Sample_series_id | GSE17300
| | Sample_data_row_count | 16569
| | |
|
GSM432927 | GPL570 |
|
USF1 replicate 2
|
HEK293T cell line
|
cell line: HEK293T
|
n/a
|
| Sample_geo_accession | GSM432927
| | Sample_status | Public on Sep 14 2009
| | Sample_submission_date | Jul 24 2009
| | Sample_last_update_date | Sep 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was collected using the RNeasy Plus Mini Kit (Cat No. 74134) 48 hours after transient transfection of HEK293T cells.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were then converted to cRNA probes using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).
| | Sample_hyb_protocol | The cRNA probes were then hybridized using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).
| | Sample_scan_protocol | The chips were scanned using the GeneArray scanner (Affymetrix) to produce CEL files.
| | Sample_data_processing | A rigorous quality control pipeline was developed to prepare the gene expression microarray data for analysis. First, the CEL files were imported into R 2.8.0 using the justRMA function of the Affymetrix library from Bioconductor, which applies background subtraction and quantile normalization. An alternate CDF file (U133Plus2msk.cdf.gz) was used to exclude mis-targeted and nonspecific probes from the microarrays (Zhang et al. 2005), and probesets with less than 7 remaining probes were also excluded. Probesets with more than 50% absent calls were excluded, as calculated using the panp package from Bioconductor. Finally, the ComBat library in R was used to correct for batch effect (Johnson et al. 2007).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Christopher,L,Plaisier
| | Sample_contact_email | plaisier@ucla.edu
| | Sample_contact_phone | 310 794-9802
| | Sample_contact_fax | 310 794-5446
| | Sample_contact_laboratory | Paivi Pajukanta
| | Sample_contact_department | Human Genetics
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 695 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095-7088
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432927/suppl/GSM432927.CEL.gz
| | Sample_series_id | GSE17300
| | Sample_data_row_count | 16569
| | |
|
GSM432928 | GPL570 |
|
USF1 replicate 3
|
HEK293T cell line
|
cell line: HEK293T
|
n/a
|
| Sample_geo_accession | GSM432928
| | Sample_status | Public on Sep 14 2009
| | Sample_submission_date | Jul 24 2009
| | Sample_last_update_date | Sep 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was collected using the RNeasy Plus Mini Kit (Cat No. 74134) 48 hours after transient transfection of HEK293T cells.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were then converted to cRNA probes using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).
| | Sample_hyb_protocol | The cRNA probes were then hybridized using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).
| | Sample_scan_protocol | The chips were scanned using the GeneArray scanner (Affymetrix) to produce CEL files.
| | Sample_data_processing | A rigorous quality control pipeline was developed to prepare the gene expression microarray data for analysis. First, the CEL files were imported into R 2.8.0 using the justRMA function of the Affymetrix library from Bioconductor, which applies background subtraction and quantile normalization. An alternate CDF file (U133Plus2msk.cdf.gz) was used to exclude mis-targeted and nonspecific probes from the microarrays (Zhang et al. 2005), and probesets with less than 7 remaining probes were also excluded. Probesets with more than 50% absent calls were excluded, as calculated using the panp package from Bioconductor. Finally, the ComBat library in R was used to correct for batch effect (Johnson et al. 2007).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Christopher,L,Plaisier
| | Sample_contact_email | plaisier@ucla.edu
| | Sample_contact_phone | 310 794-9802
| | Sample_contact_fax | 310 794-5446
| | Sample_contact_laboratory | Paivi Pajukanta
| | Sample_contact_department | Human Genetics
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 695 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095-7088
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432928/suppl/GSM432928.CEL.gz
| | Sample_series_id | GSE17300
| | Sample_data_row_count | 16569
| | |
|
GSM432929 | GPL570 |
|
Empty vector replicate 1
|
HEK293T cell line
|
cell line: HEK293T
|
n/a
|
| Sample_geo_accession | GSM432929
| | Sample_status | Public on Sep 14 2009
| | Sample_submission_date | Jul 24 2009
| | Sample_last_update_date | Sep 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was collected using the RNeasy Plus Mini Kit (Cat No. 74134) 48 hours after transient transfection of HEK293T cells.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were then converted to cRNA probes using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).
| | Sample_hyb_protocol | The cRNA probes were then hybridized using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).
| | Sample_scan_protocol | The chips were scanned using the GeneArray scanner (Affymetrix) to produce CEL files.
| | Sample_data_processing | A rigorous quality control pipeline was developed to prepare the gene expression microarray data for analysis. First, the CEL files were imported into R 2.8.0 using the justRMA function of the Affymetrix library from Bioconductor, which applies background subtraction and quantile normalization. An alternate CDF file (U133Plus2msk.cdf.gz) was used to exclude mis-targeted and nonspecific probes from the microarrays (Zhang et al. 2005), and probesets with less than 7 remaining probes were also excluded. Probesets with more than 50% absent calls were excluded, as calculated using the panp package from Bioconductor. Finally, the ComBat library in R was used to correct for batch effect (Johnson et al. 2007).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Christopher,L,Plaisier
| | Sample_contact_email | plaisier@ucla.edu
| | Sample_contact_phone | 310 794-9802
| | Sample_contact_fax | 310 794-5446
| | Sample_contact_laboratory | Paivi Pajukanta
| | Sample_contact_department | Human Genetics
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 695 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095-7088
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432929/suppl/GSM432929.CEL.gz
| | Sample_series_id | GSE17300
| | Sample_data_row_count | 16569
| | |
|
GSM432930 | GPL570 |
|
Empty vector replicate 2
|
HEK293T cell line
|
cell line: HEK293T
|
n/a
|
| Sample_geo_accession | GSM432930
| | Sample_status | Public on Sep 14 2009
| | Sample_submission_date | Jul 24 2009
| | Sample_last_update_date | Sep 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was collected using the RNeasy Plus Mini Kit (Cat No. 74134) 48 hours after transient transfection of HEK293T cells.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were then converted to cRNA probes using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).
| | Sample_hyb_protocol | The cRNA probes were then hybridized using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).
| | Sample_scan_protocol | The chips were scanned using the GeneArray scanner (Affymetrix) to produce CEL files.
| | Sample_data_processing | A rigorous quality control pipeline was developed to prepare the gene expression microarray data for analysis. First, the CEL files were imported into R 2.8.0 using the justRMA function of the Affymetrix library from Bioconductor, which applies background subtraction and quantile normalization. An alternate CDF file (U133Plus2msk.cdf.gz) was used to exclude mis-targeted and nonspecific probes from the microarrays (Zhang et al. 2005), and probesets with less than 7 remaining probes were also excluded. Probesets with more than 50% absent calls were excluded, as calculated using the panp package from Bioconductor. Finally, the ComBat library in R was used to correct for batch effect (Johnson et al. 2007).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Christopher,L,Plaisier
| | Sample_contact_email | plaisier@ucla.edu
| | Sample_contact_phone | 310 794-9802
| | Sample_contact_fax | 310 794-5446
| | Sample_contact_laboratory | Paivi Pajukanta
| | Sample_contact_department | Human Genetics
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 695 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095-7088
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432930/suppl/GSM432930.CEL.gz
| | Sample_series_id | GSE17300
| | Sample_data_row_count | 16569
| | |
|
GSM432931 | GPL570 |
|
Empty vector replicate 3
|
HEK293T cell line
|
cell line: HEK293T
|
n/a
|
| Sample_geo_accession | GSM432931
| | Sample_status | Public on Sep 14 2009
| | Sample_submission_date | Jul 24 2009
| | Sample_last_update_date | Sep 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was collected using the RNeasy Plus Mini Kit (Cat No. 74134) 48 hours after transient transfection of HEK293T cells.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were then converted to cRNA probes using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).
| | Sample_hyb_protocol | The cRNA probes were then hybridized using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).
| | Sample_scan_protocol | The chips were scanned using the GeneArray scanner (Affymetrix) to produce CEL files.
| | Sample_data_processing | A rigorous quality control pipeline was developed to prepare the gene expression microarray data for analysis. First, the CEL files were imported into R 2.8.0 using the justRMA function of the Affymetrix library from Bioconductor, which applies background subtraction and quantile normalization. An alternate CDF file (U133Plus2msk.cdf.gz) was used to exclude mis-targeted and nonspecific probes from the microarrays (Zhang et al. 2005), and probesets with less than 7 remaining probes were also excluded. Probesets with more than 50% absent calls were excluded, as calculated using the panp package from Bioconductor. Finally, the ComBat library in R was used to correct for batch effect (Johnson et al. 2007).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Christopher,L,Plaisier
| | Sample_contact_email | plaisier@ucla.edu
| | Sample_contact_phone | 310 794-9802
| | Sample_contact_fax | 310 794-5446
| | Sample_contact_laboratory | Paivi Pajukanta
| | Sample_contact_department | Human Genetics
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 695 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095-7088
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432931/suppl/GSM432931.CEL.gz
| | Sample_series_id | GSE17300
| | Sample_data_row_count | 16569
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