Search results for the GEO ID: GSE17827  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM444777 | GPL570 |
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IMR32, MEIS1-shRNA, t=0h
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IMR32, MEIS1-shRNA, time 0h
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cell line: IMR32
cell type: Neuroblastoma
stable shrna: inducible MEIS1-shRNA
doxycycline induction: no
induction time: 0h
|
Neuroblastoma cells were stably transfected with shRNA specific for MEIS1b. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
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| Sample_geo_accession | GSM444777
| | Sample_status | Public on Sep 24 2012
| | Sample_submission_date | Aug 26 2009
| | Sample_last_update_date | Sep 24 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | To induce MEIS1-shRNA in IMR32, doxycycline was addded to the medium. Controls were identically grown but without doxycycline.
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix). The VALUEs in the data table represent log2 MAS5.0 signal intensities.
| | 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/GSM444nnn/GSM444777/suppl/GSM444777.CEL.gz
| | Sample_series_id | GSE17827
| | Sample_series_id | GSE18272
| | Sample_data_row_count | 54675
| | |
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GSM444778 | GPL570 |
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IMR32, MEIS1-shRNA, t=24h
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IMR32, MEIS1-shRNA, time 24h
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cell line: IMR32
cell type: Neuroblastoma
stable shrna: inducible MEIS1-shRNA
doxycycline induction: yes
induction time: 24h
|
Neuroblastoma cells were stably transfected with shRNA specific for MEIS1b. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM444778
| | Sample_status | Public on Sep 24 2012
| | Sample_submission_date | Aug 26 2009
| | Sample_last_update_date | Sep 24 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | To induce MEIS1-shRNA in IMR32, doxycycline was addded to the medium. Controls were identically grown but without doxycycline.
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix). The VALUEs in the data table represent log2 MAS5.0 signal intensities.
| | 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/GSM444nnn/GSM444778/suppl/GSM444778.CEL.gz
| | Sample_series_id | GSE17827
| | Sample_series_id | GSE18272
| | Sample_data_row_count | 54675
| | |
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GSM444779 | GPL570 |
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IMR32, MEIS1-shRNA, t=48h
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IMR32, MEIS1-shRNA, time 48h
|
cell line: IMR32
cell type: Neuroblastoma
stable shrna: inducible MEIS1-shRNA
doxycycline induction: yes
induction time: 48h
|
Neuroblastoma cells were stably transfected with shRNA specific for MEIS1b. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM444779
| | Sample_status | Public on Sep 24 2012
| | Sample_submission_date | Aug 26 2009
| | Sample_last_update_date | Sep 24 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | To induce MEIS1-shRNA in IMR32, doxycycline was addded to the medium. Controls were identically grown but without doxycycline.
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix). The VALUEs in the data table represent log2 MAS5.0 signal intensities.
| | 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/GSM444nnn/GSM444779/suppl/GSM444779.CEL.gz
| | Sample_series_id | GSE17827
| | Sample_series_id | GSE18272
| | Sample_data_row_count | 54675
| | |
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GSM444780 | GPL570 |
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IMR32, MEIS1-shRNA, t=96h
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IMR32, MEIS1-shRNA, time 96h
|
cell line: IMR32
cell type: Neuroblastoma
stable shrna: inducible MEIS1-shRNA
doxycycline induction: yes
induction time: 96h
|
Neuroblastoma cells were stably transfected with shRNA specific for MEIS1b. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM444780
| | Sample_status | Public on Sep 24 2012
| | Sample_submission_date | Aug 26 2009
| | Sample_last_update_date | Sep 24 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | To induce MEIS1-shRNA in IMR32, doxycycline was addded to the medium. Controls were identically grown but without doxycycline.
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix). The VALUEs in the data table represent log2 MAS5.0 signal intensities.
| | 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/GSM444nnn/GSM444780/suppl/GSM444780.CEL.gz
| | Sample_series_id | GSE17827
| | Sample_series_id | GSE18272
| | Sample_data_row_count | 54675
| | |
|
GSM444781 | GPL570 |
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IMR32, MEIS1-shRNA, t=192h
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IMR32, MEIS1-shRNA, time 192h
|
cell line: IMR32
cell type: Neuroblastoma
stable shrna: inducible MEIS1-shRNA
doxycycline induction: yes
induction time: 192h
|
Neuroblastoma cells were stably transfected with shRNA specific for MEIS1b. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM444781
| | Sample_status | Public on Sep 24 2012
| | Sample_submission_date | Aug 26 2009
| | Sample_last_update_date | Sep 24 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | To induce MEIS1-shRNA in IMR32, doxycycline was addded to the medium. Controls were identically grown but without doxycycline.
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix). The VALUEs in the data table represent log2 MAS5.0 signal intensities.
| | 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/GSM444nnn/GSM444781/suppl/GSM444781.CEL.gz
| | Sample_series_id | GSE17827
| | Sample_series_id | GSE18272
| | Sample_data_row_count | 54675
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