Search results for the GEO ID: GSE8646  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM214181 | GPL570 |
|
TAp63 alpha Q540L 24h induction s1
|
TET-on Human lung carcinoma H1299
|
Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on
|
None
|
| Sample_geo_accession | GSM214181
| | Sample_status | Public on Aug 02 2007
| | Sample_submission_date | Aug 01 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 1 μg/ml doxycycline for 24 hours
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA (ttlRNA) was extracted and
| | Sample_extract_protocol_ch1 | purified from stably transfected H1299 cell lines with the Concert
| | Sample_extract_protocol_ch1 | Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
| | Sample_extract_protocol_ch1 | with a Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
| | Sample_hyb_protocol | Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
| | Sample_hyb_protocol | (20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
| | Sample_hyb_protocol | by the manufacturer (Affymetrix Inc.).
| | Sample_scan_protocol | GeneChip Fluidics station 400
| | Sample_scan_protocol | (Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.
| | Sample_data_processing | DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
| | Sample_data_processing | Probe set intensities were obtained by means of GCRMA, a robust
| | Sample_data_processing | multiarray analysis method.
| | Sample_data_processing | The full data set was normalized according to the
| | Sample_data_processing | quantiles method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM214nnn/GSM214181/suppl/GSM214181.CEL.gz
| | Sample_series_id | GSE8646
| | Sample_data_row_count | 54675
| | |
|
GSM214184 | GPL570 |
|
TAp63 alpha Q540L 24h induction s2
|
TET-on Human lung carcinoma H1299
|
Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on
|
None
|
| Sample_geo_accession | GSM214184
| | Sample_status | Public on Aug 02 2007
| | Sample_submission_date | Aug 01 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 1 μg/ml doxycycline for 24 hours
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA (ttlRNA) was extracted and
| | Sample_extract_protocol_ch1 | purified from stably transfected H1299 cell lines with the Concert
| | Sample_extract_protocol_ch1 | Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
| | Sample_extract_protocol_ch1 | with a Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
| | Sample_hyb_protocol | Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
| | Sample_hyb_protocol | (20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
| | Sample_hyb_protocol | by the manufacturer (Affymetrix Inc.).
| | Sample_scan_protocol | GeneChip Fluidics station 400
| | Sample_scan_protocol | (Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.
| | Sample_data_processing | DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
| | Sample_data_processing | Probe set intensities were obtained by means of GCRMA, a robust
| | Sample_data_processing | multiarray analysis method.
| | Sample_data_processing | The full data set was normalized according to the
| | Sample_data_processing | quantiles method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM214nnn/GSM214184/suppl/GSM214184.CEL.gz
| | Sample_series_id | GSE8646
| | Sample_data_row_count | 54675
| | |
|
GSM214186 | GPL570 |
|
TAp63 alpha 24h induction s1
|
TET-on Human lung carcinoma H1299
|
Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on
|
None
|
| Sample_geo_accession | GSM214186
| | Sample_status | Public on Aug 02 2007
| | Sample_submission_date | Aug 01 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 1 μg/ml doxycycline for 24 hours
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA (ttlRNA) was extracted and
| | Sample_extract_protocol_ch1 | purified from stably transfected H1299 cell lines with the Concert
| | Sample_extract_protocol_ch1 | Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
| | Sample_extract_protocol_ch1 | with a Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
| | Sample_hyb_protocol | Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
| | Sample_hyb_protocol | (20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
| | Sample_hyb_protocol | by the manufacturer (Affymetrix Inc.).
| | Sample_scan_protocol | GeneChip Fluidics station 400
| | Sample_scan_protocol | (Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.
| | Sample_data_processing | DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
| | Sample_data_processing | Probe set intensities were obtained by means of GCRMA, a robust
| | Sample_data_processing | multiarray analysis method.
| | Sample_data_processing | The full data set was normalized according to the
| | Sample_data_processing | quantiles method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM214nnn/GSM214186/suppl/GSM214186.CEL.gz
| | Sample_series_id | GSE8646
| | Sample_data_row_count | 54675
| | |
|
GSM214187 | GPL570 |
|
TAp63 alpha 24h induction s2
|
TET-on Human lung carcinoma H1299
|
Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on
|
None
|
| Sample_geo_accession | GSM214187
| | Sample_status | Public on Aug 02 2007
| | Sample_submission_date | Aug 01 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 1 μg/ml doxycycline for 24 hours
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA (ttlRNA) was extracted and
| | Sample_extract_protocol_ch1 | purified from stably transfected H1299 cell lines with the Concert
| | Sample_extract_protocol_ch1 | Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
| | Sample_extract_protocol_ch1 | with a Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
| | Sample_hyb_protocol | Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
| | Sample_hyb_protocol | (20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
| | Sample_hyb_protocol | by the manufacturer (Affymetrix Inc.).
| | Sample_scan_protocol | GeneChip Fluidics station 400
| | Sample_scan_protocol | (Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.
| | Sample_data_processing | DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
| | Sample_data_processing | Probe set intensities were obtained by means of GCRMA, a robust
| | Sample_data_processing | multiarray analysis method.
| | Sample_data_processing | The full data set was normalized according to the
| | Sample_data_processing | quantiles method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM214nnn/GSM214187/suppl/GSM214187.CEL.gz
| | Sample_series_id | GSE8646
| | Sample_data_row_count | 54675
| | |
|
GSM214200 | GPL570 |
|
TAp63 alpha 24h induction s3
|
TET-on Human lung carcinoma H1299
|
Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on
|
None
|
| Sample_geo_accession | GSM214200
| | Sample_status | Public on Aug 02 2007
| | Sample_submission_date | Aug 01 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 1 μg/ml doxycycline for 24 hours
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA (ttlRNA) was extracted and
| | Sample_extract_protocol_ch1 | purified from stably transfected H1299 cell lines with the Concert
| | Sample_extract_protocol_ch1 | Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
| | Sample_extract_protocol_ch1 | with a Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
| | Sample_hyb_protocol | Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
| | Sample_hyb_protocol | (20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
| | Sample_hyb_protocol | by the manufacturer (Affymetrix Inc.).
| | Sample_scan_protocol | GeneChip Fluidics station 400
| | Sample_scan_protocol | (Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.
| | Sample_data_processing | DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
| | Sample_data_processing | Probe set intensities were obtained by means of GCRMA, a robust
| | Sample_data_processing | multiarray analysis method.
| | Sample_data_processing | The full data set was normalized according to the
| | Sample_data_processing | quantiles method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM214nnn/GSM214200/suppl/GSM214200.CEL.gz
| | Sample_series_id | GSE8646
| | Sample_data_row_count | 54675
| | |
|
GSM214202 | GPL570 |
|
TAp63 alpha Q540L 24h without induction s1
|
TET-on Human lung carcinoma H1299
|
Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on
|
None
|
| Sample_geo_accession | GSM214202
| | Sample_status | Public on Aug 02 2007
| | Sample_submission_date | Aug 01 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | None
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA (ttlRNA) was extracted and
| | Sample_extract_protocol_ch1 | purified from stably transfected H1299 cell lines with the Concert
| | Sample_extract_protocol_ch1 | Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
| | Sample_extract_protocol_ch1 | with a Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
| | Sample_hyb_protocol | Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
| | Sample_hyb_protocol | (20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
| | Sample_hyb_protocol | by the manufacturer (Affymetrix Inc.).
| | Sample_scan_protocol | GeneChip Fluidics station 400
| | Sample_scan_protocol | (Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.
| | Sample_data_processing | DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
| | Sample_data_processing | Probe set intensities were obtained by means of GCRMA, a robust
| | Sample_data_processing | multiarray analysis method.
| | Sample_data_processing | The full data set was normalized according to the
| | Sample_data_processing | quantiles method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM214nnn/GSM214202/suppl/GSM214202.CEL.gz
| | Sample_series_id | GSE8646
| | Sample_data_row_count | 54675
| | |
|
GSM214243 | GPL570 |
|
TAp63 alpha Q540L 24h without induction s2
|
TET-on Human lung carcinoma H1299
|
Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on
|
None
|
| Sample_geo_accession | GSM214243
| | Sample_status | Public on Aug 02 2007
| | Sample_submission_date | Aug 01 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | None
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA (ttlRNA) was extracted and
| | Sample_extract_protocol_ch1 | purified from stably transfected H1299 cell lines with the Concert
| | Sample_extract_protocol_ch1 | Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
| | Sample_extract_protocol_ch1 | with a Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
| | Sample_hyb_protocol | Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
| | Sample_hyb_protocol | (20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
| | Sample_hyb_protocol | by the manufacturer (Affymetrix Inc.).
| | Sample_scan_protocol | GeneChip Fluidics station 400
| | Sample_scan_protocol | (Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.
| | Sample_data_processing | DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
| | Sample_data_processing | Probe set intensities were obtained by means of GCRMA, a robust
| | Sample_data_processing | multiarray analysis method.
| | Sample_data_processing | The full data set was normalized according to the
| | Sample_data_processing | quantiles method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM214nnn/GSM214243/suppl/GSM214243.CEL.gz
| | Sample_series_id | GSE8646
| | Sample_data_row_count | 54675
| | |
|
GSM214244 | GPL570 |
|
TAp63 alpha Q540L 24h without induction s3
|
TET-on Human lung carcinoma H1299
|
Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on
|
None
|
| Sample_geo_accession | GSM214244
| | Sample_status | Public on Aug 02 2007
| | Sample_submission_date | Aug 01 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | None
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA (ttlRNA) was extracted and
| | Sample_extract_protocol_ch1 | purified from stably transfected H1299 cell lines with the Concert
| | Sample_extract_protocol_ch1 | Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
| | Sample_extract_protocol_ch1 | with a Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
| | Sample_hyb_protocol | Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
| | Sample_hyb_protocol | (20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
| | Sample_hyb_protocol | by the manufacturer (Affymetrix Inc.).
| | Sample_scan_protocol | GeneChip Fluidics station 400
| | Sample_scan_protocol | (Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.
| | Sample_data_processing | DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
| | Sample_data_processing | Probe set intensities were obtained by means of GCRMA, a robust
| | Sample_data_processing | multiarray analysis method.
| | Sample_data_processing | The full data set was normalized according to the
| | Sample_data_processing | quantiles method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM214nnn/GSM214244/suppl/GSM214244.CEL.gz
| | Sample_series_id | GSE8646
| | Sample_data_row_count | 54675
| | |
|
GSM214245 | GPL570 |
|
TAp63 alpha 24h without induction s1
|
TET-on Human lung carcinoma H1299
|
Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on
|
None
|
| Sample_geo_accession | GSM214245
| | Sample_status | Public on Aug 02 2007
| | Sample_submission_date | Aug 01 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | None
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA (ttlRNA) was extracted and
| | Sample_extract_protocol_ch1 | purified from stably transfected H1299 cell lines with the Concert
| | Sample_extract_protocol_ch1 | Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
| | Sample_extract_protocol_ch1 | with a Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
| | Sample_hyb_protocol | Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
| | Sample_hyb_protocol | (20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
| | Sample_hyb_protocol | by the manufacturer (Affymetrix Inc.).
| | Sample_scan_protocol | GeneChip Fluidics station 400
| | Sample_scan_protocol | (Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.
| | Sample_data_processing | DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
| | Sample_data_processing | Probe set intensities were obtained by means of GCRMA, a robust
| | Sample_data_processing | multiarray analysis method.
| | Sample_data_processing | The full data set was normalized according to the
| | Sample_data_processing | quantiles method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM214nnn/GSM214245/suppl/GSM214245.CEL.gz
| | Sample_series_id | GSE8646
| | Sample_data_row_count | 54675
| | |
|
GSM214246 | GPL570 |
|
TAp63 alpha 24h without induction s2
|
TET-on Human lung carcinoma H1299
|
Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on
|
None
|
| Sample_geo_accession | GSM214246
| | Sample_status | Public on Aug 02 2007
| | Sample_submission_date | Aug 01 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | None
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA (ttlRNA) was extracted and
| | Sample_extract_protocol_ch1 | purified from stably transfected H1299 cell lines with the Concert
| | Sample_extract_protocol_ch1 | Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
| | Sample_extract_protocol_ch1 | with a Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
| | Sample_hyb_protocol | Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
| | Sample_hyb_protocol | (20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
| | Sample_hyb_protocol | by the manufacturer (Affymetrix Inc.).
| | Sample_scan_protocol | GeneChip Fluidics station 400
| | Sample_scan_protocol | (Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.
| | Sample_data_processing | DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
| | Sample_data_processing | Probe set intensities were obtained by means of GCRMA, a robust
| | Sample_data_processing | multiarray analysis method.
| | Sample_data_processing | The full data set was normalized according to the
| | Sample_data_processing | quantiles method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM214nnn/GSM214246/suppl/GSM214246.CEL.gz
| | Sample_series_id | GSE8646
| | Sample_data_row_count | 54675
| | |
|
GSM214248 | GPL570 |
|
TAp63 alpha 24h without induction s3
|
TET-on Human lung carcinoma H1299
|
Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on
|
None
|
| Sample_geo_accession | GSM214248
| | Sample_status | Public on Aug 02 2007
| | Sample_submission_date | Aug 01 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | None
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA (ttlRNA) was extracted and
| | Sample_extract_protocol_ch1 | purified from stably transfected H1299 cell lines with the Concert
| | Sample_extract_protocol_ch1 | Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
| | Sample_extract_protocol_ch1 | with a Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).
| | Sample_hyb_protocol | Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
| | Sample_hyb_protocol | (20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
| | Sample_hyb_protocol | by the manufacturer (Affymetrix Inc.).
| | Sample_scan_protocol | GeneChip Fluidics station 400
| | Sample_scan_protocol | (Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.
| | Sample_data_processing | DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
| | Sample_data_processing | Probe set intensities were obtained by means of GCRMA, a robust
| | Sample_data_processing | multiarray analysis method.
| | Sample_data_processing | The full data set was normalized according to the
| | Sample_data_processing | quantiles method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM214nnn/GSM214248/suppl/GSM214248.CEL.gz
| | Sample_series_id | GSE8646
| | Sample_data_row_count | 54675
| | |
|
| |
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