Search results for the GEO ID: GSE8866  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM220186 | GPL570 |
|
IMR-32 ,T=0, 1
|
IMR-32
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220186
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220186/suppl/GSM220186.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220186/suppl/GSM220186.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
|
GSM220187 | GPL570 |
|
imr-32,GFP,T=48, 1
|
imr-32
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220187
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220187/suppl/GSM220187.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220187/suppl/GSM220187.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
|
GSM220188 | GPL570 |
|
imr-32,ccnd1 siRNA,T=48, 1
|
imr-32
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220188
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220188/suppl/GSM220188.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220188/suppl/GSM220188.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
|
GSM220189 | GPL570 |
|
imr-32,gfp siRNA,T=48,2
|
imr-32
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220189
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220189/suppl/GSM220189.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220189/suppl/GSM220189.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
|
GSM220191 | GPL570 |
|
imr-32,cdk4 siRNA,t=48, 2
|
imr-32
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220191
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220191/suppl/GSM220191.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220191/suppl/GSM220191.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
|
GSM220199 | GPL570 |
|
imr-32,t=0,2
|
imr-32
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220199
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220199/suppl/GSM220199.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220199/suppl/GSM220199.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
|
GSM220203 | GPL570 |
|
imr-32,t=0,3
|
imr-32
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220203
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220203/suppl/GSM220203.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220203/suppl/GSM220203.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
|
GSM220205 | GPL570 |
|
imr-32,gfp siRNA,t=48,3
|
imr-32
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220205
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220205/suppl/GSM220205.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220205/suppl/GSM220205.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
|
GSM220206 | GPL570 |
|
imr-32,ccnd1 siRNA,t=48,3
|
imr-32,
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220206
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220206/suppl/GSM220206.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220206/suppl/GSM220206.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
|
GSM220207 | GPL570 |
|
imr-32,cdk4 siRNA,t=48,3
|
imr-32
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220207
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220207/suppl/GSM220207.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220207/suppl/GSM220207.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
|
GSM220208 | GPL570 |
|
imr-32,gfp siRNA, t=48, 4
|
imr-32
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220208
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220208/suppl/GSM220208.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220208/suppl/GSM220208.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
|
GSM220209 | GPL570 |
|
imr-32,ccnd1siRNA, t=48, 4
|
imr-32
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220209
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220209/suppl/GSM220209.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220209/suppl/GSM220209.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
|
GSM220210 | GPL570 |
|
imr-32, cdk4 siRNA, t=48, 4
|
imr-32
|
Neuroblastoma cell line
|
Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil
|
| Sample_geo_accession | GSM220210
| | Sample_status | Public on Aug 20 2008
| | Sample_submission_date | Aug 23 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_biomaterial_provider_ch1 | Human Genetics, Academic Medical Centre, Amsterdam
| | Sample_treatment_protocol_ch1 | IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).
| | Sample_growth_protocol_ch1 | IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220210/suppl/GSM220210.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM220nnn/GSM220210/suppl/GSM220210.CHP.gz
| | Sample_series_id | GSE8866
| | Sample_data_row_count | 54675
| | |
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