Search results for the GEO ID: GSE18668  |
(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 |
GSM586978 | GPL570 |
|
TC-797, post-etoh, rep 1
|
TC-797, post-etoh, rep 1
|
cell line: NMC cell line TC-797
agent: ethanol vehicle control
|
Gene expression data from TC-797 NMC cell line cells 24 hours post treatment with ethanol vehicle control
797-etoh-1-1567D.CEL
|
| Sample_geo_accession | GSM586978
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586978/suppl/GSM586978.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586979 | GPL570 |
|
TC-797, post-etoh, rep 2
|
TC-797, post-etoh, rep 2
|
cell line: NMC cell line TC-797
agent: ethanol vehicle control
|
Gene expression data from TC-797 NMC cell line cells 24 hours post treatment with ethanol vehicle control
797-etoh-2-1567E.CEL
|
| Sample_geo_accession | GSM586979
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586979/suppl/GSM586979.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586980 | GPL570 |
|
TC-797, post-etoh, rep 3
|
TC-797, post-etoh, rep 3
|
cell line: NMC cell line TC-797
agent: ethanol vehicle control
|
Gene expression data from TC-797 NMC cell line cells 24 hours post treatment with ethanol vehicle control
797-etoh-3-1567F.CEL
|
| Sample_geo_accession | GSM586980
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586980/suppl/GSM586980.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586981 | GPL570 |
|
TC-797, post-TSA, rep 1
|
TC-797, post-TSA, rep 1
|
cell line: NMC cell line TC-797
agent: trichostatin (TSA)
|
Gene expression data from TC-797 NMC cell line cells 23 hours treatment with 25nM trichostatin (TSA)
797-tsa-1-1567A.CEL
|
| Sample_geo_accession | GSM586981
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586981/suppl/GSM586981.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586982 | GPL570 |
|
TC-797, post-TSA, rep 2
|
TC-797, post-TSA, rep 2
|
cell line: NMC cell line TC-797
agent: trichostatin (TSA)
|
Gene expression data from TC-797 NMC cell line cells 23 hours treatment with 25nM trichostatin (TSA)
797-tsa-2-1567B.CEL
|
| Sample_geo_accession | GSM586982
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586982/suppl/GSM586982.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586983 | GPL570 |
|
TC-797, post-TSA, rep 3
|
TC-797, post-TSA, rep 3
|
cell line: NMC cell line TC-797
agent: trichostatin (TSA)
|
Gene expression data from TC-797 NMC cell line cells 23 hours treatment with 25nM trichostatin (TSA)
797-tsa-3-1567C.CEL
|
| Sample_geo_accession | GSM586983
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586983/suppl/GSM586983.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586984 | GPL570 |
|
TC-797, post control siRNA, rep 1
|
TC-797, post control siRNA, rep 1
|
cell line: NMC cell line TC-797
agent: scrambled control siRNA
|
Gene expression data from TC-797 NMC cell line cells 23 hours post transfection with scrambled control siRNA
797_CTRL_siRNA_1.CEL
|
| Sample_geo_accession | GSM586984
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586984/suppl/GSM586984.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586985 | GPL570 |
|
TC-797, post control siRNA, rep 2
|
TC-797, post control siRNA, rep 2
|
cell line: NMC cell line TC-797
agent: scrambled control siRNA
|
Gene expression data from TC-797 NMC cell line cells 23 hours post transfection with scrambled control siRNA
797_CTRL_siRNA_2.CEL
|
| Sample_geo_accession | GSM586985
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586985/suppl/GSM586985.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586986 | GPL570 |
|
TC-797, post NUT siRNA, rep 1
|
TC-797, post NUT siRNA, rep 1
|
cell line: NMC cell line TC-797
agent: NUT siRNA
|
Gene expression data from TC-797 NMC cell line cells 23 hours post transfection with NUT siRNA
797_NUT_siRNA_1.CEL
|
| Sample_geo_accession | GSM586986
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586986/suppl/GSM586986.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586988 | GPL570 |
|
PER-403, POST-ETOH, rep1
|
PER-403, POST-ETOH, rep1
|
cell line: NMC cell line PER-403
agent: ethanol vehicle control
|
Gene expression data from PER-403 NMC cell line cells 24 hours post treatment with ethanol vehicle control
per403-etoh-1-1567J.CEL
|
| Sample_geo_accession | GSM586988
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586988/suppl/GSM586988.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586989 | GPL570 |
|
PER-403, POST-ETOH, rep2
|
PER-403, POST-ETOH, rep2
|
cell line: NMC cell line PER-403
agent: ethanol vehicle control
|
Gene expression data from PER-403 NMC cell line cells 24 hours post treatment with ethanol vehicle control
per403-etoh-2-1567K.CEL
|
| Sample_geo_accession | GSM586989
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586989/suppl/GSM586989.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586990 | GPL570 |
|
PER-403, POST-ETOH, rep3
|
PER-403, POST-ETOH, rep3
|
cell line: NMC cell line PER-403
agent: ethanol vehicle control
|
Gene expression data from PER-403 NMC cell line cells 24 hours post treatment with ethanol vehicle control
per403-etoh-3-1567L.CEL
|
| Sample_geo_accession | GSM586990
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586990/suppl/GSM586990.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586991 | GPL570 |
|
PER-403, POST-TSA, rep 1
|
PER-403, POST-TSA, rep 1
|
cell line: NMC cell line PER-403
agent: trichostatin (TSA)
|
Gene expression data from PER-403 NMC cell line cells 24 hours post treatment with trichostatin (TSA).
per403-tsa-1-1567G.CEL
|
| Sample_geo_accession | GSM586991
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586991/suppl/GSM586991.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586992 | GPL570 |
|
PER-403, POST-TSA, rep 2
|
PER-403, POST-TSA, rep 2
|
cell line: NMC cell line PER-403
agent: trichostatin (TSA)
|
Gene expression data from PER-403 NMC cell line cells 24 hours post treatment with trichostatin (TSA).
per403-tsa-2-1567H.CEL
|
| Sample_geo_accession | GSM586992
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586992/suppl/GSM586992.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586993 | GPL570 |
|
PER-403, POST-TSA, rep 3
|
PER-403, POST-TSA, rep 3
|
cell line: NMC cell line PER-403
agent: trichostatin (TSA)
|
Gene expression data from PER-403 NMC cell line cells 24 hours post treatment with trichostatin (TSA).
per403-tsa-3-1567I.CEL
|
| Sample_geo_accession | GSM586993
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586993/suppl/GSM586993.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586994 | GPL570 |
|
PER-403, post control siRNA, rep 1
|
PER-403, post control siRNA, rep 1
|
cell line: NMC cell line PER-403
agent: scrambled control siRNA
|
Gene expression data from PER-403 NMC cell line cells 23 hours post transfection with scrambled control siRNA
per403_CTRL_siRNA_1.CEL
|
| Sample_geo_accession | GSM586994
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586994/suppl/GSM586994.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586996 | GPL570 |
|
PER-403, post NUT siRNA, rep 1
|
PER-403, post NUT siRNA, rep 1
|
cell line: NMC cell line PER-403
agent: NUT siRNA
|
Gene expression data from PER-403 NMC cell line cells 23 hours post transfection with NUT siRNA
per403_NUT_siRNA_1.CEL
|
| Sample_geo_accession | GSM586996
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586996/suppl/GSM586996.CEL.gz
| | Sample_series_id | GSE18668
| | Sample_data_row_count | 54675
| | |
|
GSM586997 | GPL570 |
|
PER-403, post NUT siRNA, rep 2
|
PER-403, post NUT siRNA, rep 2
|
cell line: NMC cell line PER-403
agent: NUT siRNA
|
Gene expression data from PER-403 NMC cell line cells 23 hours post transfection with NUT siRNA
per403_nut_siRNA_2.CEL
|
| Sample_geo_accession | GSM586997
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Aug 25 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Transfection into NMC cell lines was performed by electroporation with a Nucleofector II device (Lonza). TSA was administered at a final concentration of 25nM.
| | Sample_growth_protocol_ch1 | The endogenous BRD4-NUT-expressing cell lines TC797 (Toretsky et al., 2003), PER-403 (Kees et al., 1991), 00-143 (French et al., 2001), and TY82 (Kuzume et al., 1992) have been described previously. TC-797 ells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% bovine growth serum (Hyclone, Logan, UT), 2 mM L-glutamine, 100 U of penicillin G/ml, and 100 mg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2. PER-403 was maintained in the same media with 1 mM sodium pyruvate (Mediatech, Herndon, VA), 0.1 mM non-essential amino acids (Invitrogen), and 40 µM β-mercaptoethanol (American Bioanalytical (Natick, MA)).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol (Invitrogen) extraction followed by RNAeasy (Qiagen) purification of total RNA was performed according to the manufacturers' instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization to Affymetrix Human Genome U133A Plus 2.0 microarray chips was carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
| | Sample_scan_protocol | Scanning is carried out on an Affymetrix Model 3000 scanner with autoloader.
| | Sample_data_processing | Data analysis was performed with dChip software (http://biosun1.harvard.edu/~cli/dchip.exe). The raw expression data were processed using the RMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,A,French
| | Sample_contact_email | cfrench@partners.org
| | Sample_contact_phone | 6177327675
| | Sample_contact_fax | 6172645169
| | Sample_contact_department | Pathology
| | Sample_contact_institute | BWH
| | Sample_contact_address | 75 francis st.
| | Sample_contact_city | boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM586nnn/GSM586997/suppl/GSM586997.CEL.gz
| | Sample_series_id | GSE18668
| | 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: |
|
|
|
