Search results for the GEO ID: GSE42762  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1049515 | GPL570 |
|
-Dox / -PI-103, replicate 1
|
SY5Y-TetR-FOXO3A cells, -Dox, -PI-103
|
cell line: SY5Y
cell type: SY5Y-TetR-FOXO3A neuroblastoma cells
pre-treatment: none
treatment: DMSO
|
NB906
No pre-treatment doxycycline, DMSO treatment for 6 hours.
|
| Sample_geo_accession | GSM1049515
| | Sample_status | Public on May 01 2013
| | Sample_submission_date | Dec 05 2012
| | Sample_last_update_date | May 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.
| | Sample_growth_protocol_ch1 | SY5Y-TetR-HA-FOXO3A 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 the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.
| | 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/GSM1049nnn/GSM1049515/suppl/GSM1049515_NB906.CEL.gz
| | Sample_series_id | GSE42762
| | Sample_data_row_count | 54675
| | |
|
GSM1049516 | GPL570 |
|
-Dox / +PI-103, replicate 1
|
SY5Y-TetR-FOXO3A cells, -Dox, +PI-103
|
cell line: SY5Y
cell type: SY5Y-TetR-FOXO3A neuroblastoma cells
pre-treatment: none
treatment: PI-103
|
NB907
No pre-treatment doxycycline, 1 uM PI-103 treament for 6 hours.
|
| Sample_geo_accession | GSM1049516
| | Sample_status | Public on May 01 2013
| | Sample_submission_date | Dec 05 2012
| | Sample_last_update_date | May 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.
| | Sample_growth_protocol_ch1 | SY5Y-TetR-HA-FOXO3A 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 the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.
| | 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/GSM1049nnn/GSM1049516/suppl/GSM1049516_NB907.CEL.gz
| | Sample_series_id | GSE42762
| | Sample_data_row_count | 54675
| | |
|
GSM1049517 | GPL570 |
|
+Dox / -PI-103, replicate 1
|
SY5Y-TetR-FOXO3A cells, +Dox, -PI-103
|
cell line: SY5Y
cell type: SY5Y-TetR-FOXO3A neuroblastoma cells
pre-treatment: doxycycline
treatment: DMSO
|
NB908
24 hour pre-treatment 0.1 ug/ml doxycycline, DMSO treatment for 6 hours.
|
| Sample_geo_accession | GSM1049517
| | Sample_status | Public on May 01 2013
| | Sample_submission_date | Dec 05 2012
| | Sample_last_update_date | May 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.
| | Sample_growth_protocol_ch1 | SY5Y-TetR-HA-FOXO3A 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 the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.
| | 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/GSM1049nnn/GSM1049517/suppl/GSM1049517_NB908.CEL.gz
| | Sample_series_id | GSE42762
| | Sample_data_row_count | 54675
| | |
|
GSM1049518 | GPL570 |
|
+Dox / +PI-103, replicate 1
|
SY5Y-TetR-FOXO3A cells, +Dox, +PI-103
|
cell line: SY5Y
cell type: SY5Y-TetR-FOXO3A neuroblastoma cells
pre-treatment: doxycycline
treatment: PI-103
|
NB909
24 hour pre-treatment 0.1 ug/ml doxycycline, 1 uM PI-103 treatment for 6 hours.
|
| Sample_geo_accession | GSM1049518
| | Sample_status | Public on May 01 2013
| | Sample_submission_date | Dec 05 2012
| | Sample_last_update_date | May 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.
| | Sample_growth_protocol_ch1 | SY5Y-TetR-HA-FOXO3A 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 the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.
| | 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/GSM1049nnn/GSM1049518/suppl/GSM1049518_NB909.CEL.gz
| | Sample_series_id | GSE42762
| | Sample_data_row_count | 54675
| | |
|
GSM1049519 | GPL570 |
|
-Dox / -PI-103, replicate 2
|
SY5Y-TetR-FOXO3A cells, -Dox, -PI-103
|
cell line: SY5Y
cell type: SY5Y-TetR-FOXO3A neuroblastoma cells
pre-treatment: none
treatment: DMSO
|
NB914
No pre-treatment doxycycline, DMSO treatment for 6 hours.
|
| Sample_geo_accession | GSM1049519
| | Sample_status | Public on May 01 2013
| | Sample_submission_date | Dec 05 2012
| | Sample_last_update_date | May 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.
| | Sample_growth_protocol_ch1 | SY5Y-TetR-HA-FOXO3A 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 the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.
| | 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/GSM1049nnn/GSM1049519/suppl/GSM1049519_NB914.CEL.gz
| | Sample_series_id | GSE42762
| | Sample_data_row_count | 54675
| | |
|
GSM1049520 | GPL570 |
|
-Dox / +PI-103, replicate 2
|
SY5Y-TetR-FOXO3A cells, -Dox, +PI-103
|
cell line: SY5Y
cell type: SY5Y-TetR-FOXO3A neuroblastoma cells
pre-treatment: none
treatment: PI-103
|
NB915
No pre-treatment doxycycline, 1 uM PI-103 treament for 6 hours.
|
| Sample_geo_accession | GSM1049520
| | Sample_status | Public on May 01 2013
| | Sample_submission_date | Dec 05 2012
| | Sample_last_update_date | May 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.
| | Sample_growth_protocol_ch1 | SY5Y-TetR-HA-FOXO3A 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 the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.
| | 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/GSM1049nnn/GSM1049520/suppl/GSM1049520_NB915.CEL.gz
| | Sample_series_id | GSE42762
| | Sample_data_row_count | 54675
| | |
|
GSM1049521 | GPL570 |
|
+Dox / -PI-103, replicate 2
|
SY5Y-TetR-FOXO3A cells, +Dox, -PI-103
|
cell line: SY5Y
cell type: SY5Y-TetR-FOXO3A neuroblastoma cells
pre-treatment: doxycycline
treatment: DMSO
|
NB916
24 hour pre-treatment 0.1 ug/ml doxycycline, DMSO treatment for 6 hours.
|
| Sample_geo_accession | GSM1049521
| | Sample_status | Public on May 01 2013
| | Sample_submission_date | Dec 05 2012
| | Sample_last_update_date | May 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.
| | Sample_growth_protocol_ch1 | SY5Y-TetR-HA-FOXO3A 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 the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.
| | 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/GSM1049nnn/GSM1049521/suppl/GSM1049521_NB916.CEL.gz
| | Sample_series_id | GSE42762
| | Sample_data_row_count | 54675
| | |
|
GSM1049522 | GPL570 |
|
+Dox / +PI-103, replicate 2
|
SY5Y-TetR-FOXO3A cells, +Dox, +PI-103
|
cell line: SY5Y
cell type: SY5Y-TetR-FOXO3A neuroblastoma cells
pre-treatment: doxycycline
treatment: PI-103
|
NB917
24 hour pre-treatment 0.1 ug/ml doxycycline, 1 uM PI-103 treatment for 6 hours.
|
| Sample_geo_accession | GSM1049522
| | Sample_status | Public on May 01 2013
| | Sample_submission_date | Dec 05 2012
| | Sample_last_update_date | May 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.
| | Sample_growth_protocol_ch1 | SY5Y-TetR-HA-FOXO3A 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 the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.
| | 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/GSM1049nnn/GSM1049522/suppl/GSM1049522_NB917.CEL.gz
| | Sample_series_id | GSE42762
| | Sample_data_row_count | 54675
| | |
|
GSM1049523 | GPL570 |
|
-Dox / -PI-103, replicate 3
|
SY5Y-TetR-FOXO3A cells, -Dox, -PI-103
|
cell line: SY5Y
cell type: SY5Y-TetR-FOXO3A neuroblastoma cells
pre-treatment: none
treatment: DMSO
|
NB942
No pre-treatment doxycycline, DMSO treatment for 6 hours.
|
| Sample_geo_accession | GSM1049523
| | Sample_status | Public on May 01 2013
| | Sample_submission_date | Dec 05 2012
| | Sample_last_update_date | May 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.
| | Sample_growth_protocol_ch1 | SY5Y-TetR-HA-FOXO3A 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 the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.
| | 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/GSM1049nnn/GSM1049523/suppl/GSM1049523_NB942.CEL.gz
| | Sample_series_id | GSE42762
| | Sample_data_row_count | 54675
| | |
|
GSM1049524 | GPL570 |
|
-Dox / +PI-103, replicate 3
|
SY5Y-TetR-FOXO3A cells, -Dox, +PI-103
|
cell line: SY5Y
cell type: SY5Y-TetR-FOXO3A neuroblastoma cells
pre-treatment: none
treatment: PI-103
|
NB943
No pre-treatment doxycycline, 1 uM PI-103 treament for 6 hours.
|
| Sample_geo_accession | GSM1049524
| | Sample_status | Public on May 01 2013
| | Sample_submission_date | Dec 05 2012
| | Sample_last_update_date | May 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.
| | Sample_growth_protocol_ch1 | SY5Y-TetR-HA-FOXO3A 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 the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.
| | 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/GSM1049nnn/GSM1049524/suppl/GSM1049524_NB943.CEL.gz
| | Sample_series_id | GSE42762
| | Sample_data_row_count | 54675
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GSM1049525 | GPL570 |
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+Dox / -PI-103, replicate 3
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SY5Y-TetR-FOXO3A cells, +Dox, -PI-103
|
cell line: SY5Y
cell type: SY5Y-TetR-FOXO3A neuroblastoma cells
pre-treatment: doxycycline
treatment: DMSO
|
NB944
24 hour pre-treatment 0.1 ug/ml doxycycline, DMSO treatment for 6 hours.
|
| Sample_geo_accession | GSM1049525
| | Sample_status | Public on May 01 2013
| | Sample_submission_date | Dec 05 2012
| | Sample_last_update_date | May 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.
| | Sample_growth_protocol_ch1 | SY5Y-TetR-HA-FOXO3A 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 the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.
| | 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/GSM1049nnn/GSM1049525/suppl/GSM1049525_NB944.CEL.gz
| | Sample_series_id | GSE42762
| | Sample_data_row_count | 54675
| | |
|
GSM1049526 | GPL570 |
|
+Dox / +PI-103, replicate 3
|
SY5Y-TetR-FOXO3A cells, +Dox, +PI-103
|
cell line: SY5Y
cell type: SY5Y-TetR-FOXO3A neuroblastoma cells
pre-treatment: doxycycline
treatment: PI-103
|
NB945
24 hour pre-treatment 0.1 ug/ml doxycycline, 1 uM PI-103 treatment for 6 hours.
|
| Sample_geo_accession | GSM1049526
| | Sample_status | Public on May 01 2013
| | Sample_submission_date | Dec 05 2012
| | Sample_last_update_date | May 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.1 ug/ml doxycycline for 24 hours (or left untreated) to induce over-expression of HA-tagged FOXO3A, and then treated with either 1 uM PI-103 or an equivalent volume of DMSO for 6 additional hours. Each condition was performed in triplicate across three months.
| | Sample_growth_protocol_ch1 | SY5Y-TetR-HA-FOXO3A 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 the manufacturer's protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the One-Cycle cDNA synthesis Kit (Affymetrix) according to the manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior to and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's protocol.
| | 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/GSM1049nnn/GSM1049526/suppl/GSM1049526_NB945.CEL.gz
| | Sample_series_id | GSE42762
| | Sample_data_row_count | 54675
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