Search results for the GEO ID: GSE22875  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM565176 | GPL570 |
|
D425-shOTX2_1, t=0
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 0 hrs
time course: 1
|
NB125
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565176
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565176/suppl/GSM565176.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565177 | GPL570 |
|
D425-shOTX2_1, t=8
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 8 hrs
time course: 1
|
NB126
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565177
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565177/suppl/GSM565177.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565178 | GPL570 |
|
D425-shOTX2_1, t=16
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 16 hrs
time course: 1
|
NB127
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565178
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565178/suppl/GSM565178.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565179 | GPL570 |
|
D425-shOTX2_1, t=24
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 24 hrs
time course: 1
|
NB128
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565179
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565179/suppl/GSM565179.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565180 | GPL570 |
|
D425-shOTX2_1, t=48
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 48 hrs
time course: 1
|
NB129
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565180
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565180/suppl/GSM565180.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565181 | GPL570 |
|
D425-shOTX2_1, t=96
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 96 hrs
time course: 1
|
NB130
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565181
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565181/suppl/GSM565181.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565182 | GPL570 |
|
D425-shOTX2_2, t=0
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 0 hrs
time course: 2
|
NB161
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565182
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565182/suppl/GSM565182.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565183 | GPL570 |
|
D425-shOTX2_2, t=8
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 8 hrs
time course: 2
|
NB162
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565183
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565183/suppl/GSM565183.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565184 | GPL570 |
|
D425-shOTX2_2, t=16
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 16 hrs
time course: 2
|
NB163
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565184
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565184/suppl/GSM565184.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565185 | GPL570 |
|
D425-shOTX2_2, t=24
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 24 hrs
time course: 2
|
NB164
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565185
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565185/suppl/GSM565185.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565186 | GPL570 |
|
D425-shOTX2_2, t=48
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 48 hrs
time course: 2
|
NB165
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565186
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565186/suppl/GSM565186.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565187 | GPL570 |
|
D425-shOTX2_2, t=96
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 96 hrs
time course: 2
|
NB166
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565187
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565187/suppl/GSM565187.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565188 | GPL570 |
|
D425-shOTX2_3, t=0
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 0 hrs
time course: 3
|
NB167
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565188
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565188/suppl/GSM565188.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565189 | GPL570 |
|
D425-shOTX2_3, t=8
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 8 hrs
time course: 3
|
NB168
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565189
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565189/suppl/GSM565189.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565190 | GPL570 |
|
D425-shOTX2_3, t=16
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 16 hrs
time course: 3
|
NB169
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565190
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565190/suppl/GSM565190.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565191 | GPL570 |
|
D425-shOTX2_3, t=24
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 24 hrs
time course: 3
|
NB170
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565191
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565191/suppl/GSM565191.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565192 | GPL570 |
|
D425-shOTX2_3, t=48
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 48 hrs
time course: 3
|
NB171
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565192
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565192/suppl/GSM565192.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565193 | GPL570 |
|
D425-shOTX2_3, t=96
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 96 hrs
time course: 3
|
NB172
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565193
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565193/suppl/GSM565193.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565194 | GPL570 |
|
D425-control, t=0
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: control
time: 0 hrs
|
NB190
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565194
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565194/suppl/GSM565194.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565195 | GPL570 |
|
D425-control, t=8
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: control
time: 8 hrs
|
NB191
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565195
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565195/suppl/GSM565195.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565196 | GPL570 |
|
D425-control, t=16
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: control
time: 16 hrs
|
NB192
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565196
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565196/suppl/GSM565196.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565197 | GPL570 |
|
D425-control, t=24
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: control
time: 24 hrs
|
NB193
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565197
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565197/suppl/GSM565197.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565198 | GPL570 |
|
D425-control, t=48
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: control
time: 48 hrs
|
NB194
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565198
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565198/suppl/GSM565198.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
|
GSM565199 | GPL570 |
|
D425-control, t=96
|
D425
|
cell line: Medulloblastoma cell line D425
protocol: control
time: 96 hrs
|
NB195
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Sample_geo_accession | GSM565199
| | Sample_status | Public on Jul 04 2012
| | Sample_submission_date | Jul 11 2010
| | Sample_last_update_date | Jul 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in MEM (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/GSM565nnn/GSM565199/suppl/GSM565199.CEL.gz
| | Sample_series_id | GSE22875
| | Sample_data_row_count | 54675
| | |
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