Search results for the GEO ID: GSE8066 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM199428 | GPL570 |
|
SKNAS-NmycER, t=0
|
SKNAS-NmycER cells
|
Cell line from neuroblastoma tumor, stably transfected with NmycER expression vector.
|
SKNAS-NmycER cells were grown under standard conditions and harvested at diferent timepoints after addition of 4-hydroxytamoxifen. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199428
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| 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 | To activate Nmyc-ER in SKNAS-NmycER, 4-hydroxy-tamoxifen was added to the medium to a final concentration of 50 nmol/l.
| Sample_growth_protocol_ch1 | SKNAS-NmycER 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199428/suppl/GSM199428.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199428/suppl/GSM199428.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199429 | GPL570 |
|
SKNAS-NmycER, t=24 hrs
|
SKNAS-NmycER cells
|
Cell line from neuroblastoma tumor, stably transfected with NmycER expression vector
|
SKNAS-NmycER cells were grown under standard conditions and harvested at diferent timepoints after addition of 4-hydroxytamoxifen. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199429
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| 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 | To activate Nmyc-ER in SKNAS-NmycER, 4-hydroxy-tamoxifen was added to the medium to a final concentration of 50 nmol/l.
| Sample_growth_protocol_ch1 | SKNAS-NmycER 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199429/suppl/GSM199429.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199429/suppl/GSM199429.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199430 | GPL570 |
|
SKNAS-NmycER, t=72 hrs
|
SKNAS-NmycER cells
|
Cell line from neuroblastoma tumor, stably transfected with NmycER expression vector.
|
SKNAS-NmycER cells were grown under standard conditions and harvested at diferent timepoints after addition of 4-hydroxytamoxifen. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199430
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| 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 | To activate Nmyc-ER in SKNAS-NmycER, 4-hydroxy-tamoxifen was added to the medium to a final concentration of 50 nmol/l.
| Sample_growth_protocol_ch1 | SKNAS-NmycER 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199430/suppl/GSM199430.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199430/suppl/GSM199430.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199431 | GPL570 |
|
SKNAS-NmycER, t=144 hrs
|
SKNAS-NmycER cells
|
Cell line from neuroblastoma tumor, stably transfected with NmycER expression vector.
|
SKNAS-NmycER cells were grown under standard conditions and harvested at diferent timepoints after addition of 4-hydroxytamoxifen. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199431
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| 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 | To activate Nmyc-ER in SKNAS-NmycER, 4-hydroxy-tamoxifen was added to the medium to a final concentration of 50 nmol/l.
| Sample_growth_protocol_ch1 | SKNAS-NmycER 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199431/suppl/GSM199431.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199431/suppl/GSM199431.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199432 | GPL570 |
|
IMR32-DKK1 c63, t=0
|
IMR32-DKK1 c63
|
Cell line from a neuroblastoma tumor, stably transfected with an inducible DKK1 expression vector
|
IMR32-DKK1 cells were grown under standard conditions. Cells were harvested, at 70% confluency, at different time points after adding doxycyclin. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199432
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| Sample_treatment_protocol_ch1 | To induce DKK1 expression in IMR32-DKK1, doxycyclin was added to the medium to a final concentration of 50 ng/ml
| Sample_growth_protocol_ch1 | IMR32-DKK1 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 LiCl/ureum 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199432/suppl/GSM199432.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199432/suppl/GSM199432.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199433 | GPL570 |
|
IMR32-DKK1 c63, t=24 hrs
|
IMR32-DKK1 c63
|
Cell line from a neuroblastoma tumor, stably transfected with an inducible DKK1 expression vector
|
IMR32-DKK1 cells were grown under standard conditions. Cells were harvested, at 70% confluency, at different time points after adding doxycyclin. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199433
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| Sample_treatment_protocol_ch1 | To induce DKK1 expression in IMR32-DKK1, doxycyclin was added to the medium to a final concentration of 50 ng/ml
| Sample_growth_protocol_ch1 | IMR32-DKK1 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 LiCl/ureum 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199433/suppl/GSM199433.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199433/suppl/GSM199433.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199434 | GPL570 |
|
IMR32-DKK1 c63, t=72 hrs
|
IMR32-DKK1 c63
|
Cell line from a neuroblastoma tumor, stably transfected with an inducible DKK1 expression vector
|
IMR32-DKK1 cells were grown under standard conditions. Cells were harvested, at 70% confluency, at different time points after adding doxycyclin. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199434
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| Sample_treatment_protocol_ch1 | To induce DKK1 expression in IMR32-DKK1, doxycyclin was added to the medium to a final concentration of 50 ng/ml
| Sample_growth_protocol_ch1 | IMR32-DKK1 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 LiCl/ureum 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199434/suppl/GSM199434.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199434/suppl/GSM199434.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199435 | GPL570 |
|
IMR32-DKK1 c63, t=288 hrs
|
IMR32-DKK1 c63
|
Cell line from a neuroblastoma tumor, stably transfected with an inducible DKK1 expression vector
|
IMR32-DKK1 cells were grown under standard conditions. Cells were harvested, at 70% confluency, at different time points after adding doxycyclin. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199435
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| Sample_treatment_protocol_ch1 | To induce DKK1 expression in IMR32-DKK1, doxycyclin was added to the medium to a final concentration of 50 ng/ml
| Sample_growth_protocol_ch1 | IMR32-DKK1 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 LiCl/ureum 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199435/suppl/GSM199435.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199435/suppl/GSM199435.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199436 | GPL570 |
|
IMR32-DKK1 c66, t=0
|
IMR32-DKK1 c66
|
Cell line from a neuroblastoma tumor, stably transfected with an inducible DKK1 expression vector
|
IMR32-DKK1 cells were grown under standard conditions. Cells were harvested, at 70% confluency, at different time points after adding doxycyclin. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199436
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| Sample_treatment_protocol_ch1 | To induce DKK1 expression in IMR32-DKK1, doxycyclin was added to the medium to a final concentration of 50 ng/ml
| Sample_growth_protocol_ch1 | IMR32-DKK1 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 LiCl/ureum 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199436/suppl/GSM199436.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199436/suppl/GSM199436.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199437 | GPL570 |
|
IMR32-DKK1 c66, t=24 hrs
|
IMR32-DKK1 c66
|
Cell line from a neuroblastoma tumor, stably transfected with an inducible MYCN expression vector
|
IMR32-DKK1 cells were grown under standard conditions. Cells were harvested, at 70% confluency, at different time points after adding doxycyclin. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199437
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| Sample_treatment_protocol_ch1 | To induce DKK1 expression in IMR32-DKK1, doxycyclin was added to the medium to a final concentration of 50 ng/ml
| Sample_growth_protocol_ch1 | IMR32-DKK1 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 LiCl/ureum 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199437/suppl/GSM199437.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199437/suppl/GSM199437.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199441 | GPL570 |
|
IMR32-DKK1 c66, t=72 hrs
|
IMR32-DKK1 c66
|
Cell line from a neuroblastoma tumor, stably transfected with an inducible DKK1 expression vector
|
IMR32-DKK1 cells were grown under standard conditions. Cells were harvested, at 70% confluency, at different time points after adding doxycyclin. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199441
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| Sample_treatment_protocol_ch1 | To induce DKK1 expression in IMR32-DKK1, doxycyclin was added to the medium to a final concentration of 50 ng/ml
| Sample_growth_protocol_ch1 | IMR32-DKK1 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 LiCl/ureum 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199441/suppl/GSM199441.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199441/suppl/GSM199441.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199442 | GPL570 |
|
IMR32-DKK1 c66, t=288 hrs
|
IMR32-DKK1 c66
|
Cell line from a neuroblastoma tumor, stably transfected with an inducible DKK1 expression vector
|
IMR32-DKK1 cells were grown under standard conditions. Cells were harvested, at 70% confluency, at different time points after adding doxycyclin. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199442
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| Sample_treatment_protocol_ch1 | To induce DKK1 expression in IMR32-DKK1, doxycyclin was added to the medium to a final concentration of 50 ng/ml
| Sample_growth_protocol_ch1 | IMR32-DKK1 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 LiCl/ureum 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199442/suppl/GSM199442.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199442/suppl/GSM199442.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199473 | GPL570 |
|
SHEP-21N, t=0
|
SHEP-21N
|
Cell line from a neuroblastoma tumor, stably transfected with an inducible MYCN expression vector
|
SHEP-21N cells were grown under standard conditions in presence of tetracycline (no MYCN expression) for two weeks. Tetracyclin was washed away and cells were harvested, at 70% confluency, at different time points after tetracycline removal. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199473
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| Sample_treatment_protocol_ch1 | Nmyc expression was switched off with 50 ng/ml tetracyclin. At t=0, tetracyclin was removed to induce MYCN
| Sample_growth_protocol_ch1 | SHEP-21N cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using LiCl/ureum 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199473/suppl/GSM199473.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199473/suppl/GSM199473.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199474 | GPL570 |
|
SHEP-21N, t=8 hrs
|
SHEP-21N
|
Cell line from a neuroblastoma tumor, stably transfected with an inducible MYCN expression vector
|
SHEP-21N cells were grown under standard conditions in presence of tetracycline (no MYCN expression) for two weeks. Tetracyclin was washed away and cells were harvested, at 70% confluency, at different time points after tetracycline removal. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199474
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| Sample_treatment_protocol_ch1 | Nmyc expression was switched off with 50 ng/ml tetracyclin. At t=0, tetracyclin was removed to induce MYCN
| Sample_growth_protocol_ch1 | SHEP-21N cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using LiCl/ureum 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199474/suppl/GSM199474.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199474/suppl/GSM199474.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199475 | GPL570 |
|
SHEP-21N, t=24 hrs
|
SHEP-21N
|
Cell line from a neuroblastoma tumor, stably transfected with an inducible MYCN expression vector
|
SHEP-21N cells were grown under standard conditions in presence of tetracycline (no MYCN expression) for two weeks. Tetracyclin was washed away and cells were harvested, at 70% confluency, at different time points after tetracycline removal. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199475
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| Sample_treatment_protocol_ch1 | Nmyc expression was switched off with 50 ng/ml tetracyclin. At t=0, tetracyclin was removed to induce MYCN
| Sample_growth_protocol_ch1 | SHEP-21N cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using LiCl/ureum 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199475/suppl/GSM199475.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199475/suppl/GSM199475.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
|
GSM199479 | GPL570 |
|
SHEP-21N, t=120 hrs
|
SHEP-21N
|
Cell line from a neuroblastoma tumor, stably transfected with an inducible MYCN expression vector
|
SHEP-21N cells were grown under standard conditions in presence of tetracycline (no MYCN expression) for two weeks. Tetracyclin was washed away and cells were harvested, at 70% confluency, at different time points after tetracycline removal. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
Sample_geo_accession | GSM199479
| Sample_status | Public on Aug 24 2007
| Sample_submission_date | Jun 08 2007
| Sample_last_update_date | Aug 24 2007
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| Sample_treatment_protocol_ch1 | Nmyc expression was switched off with 50 ng/ml tetracyclin. At t=0 , tetracyclin was removed to induce NMYC
| Sample_growth_protocol_ch1 | SHEP-21N cells were cultured in RPMI (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using LiCl/ureum 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. Labelling 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 protocol.
| Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 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/GSM199nnn/GSM199479/suppl/GSM199479.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM199nnn/GSM199479/suppl/GSM199479.CHP.gz
| Sample_series_id | GSE8066
| Sample_data_row_count | 54675
| |
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