Search results for the GEO ID: GSE7578  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM182006 | GPL570 |
|
Bmi1 shRNA, biological rep1
|
Human medulloblastoma DAOY cell line
|
Stable lentiviral shRNA
|
Gene expression data from DAOY cells stably expressing Bmi1 shRNA
|
| Sample_geo_accession | GSM182006
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182006/suppl/GSM182006.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182007 | GPL570 |
|
Bmi1 shRNA, biological rep2
|
Human medulloblastoma DAOY cell line
|
Stable lentiviral shRNA
|
Gene expression data from DAOY cells stably expressing Bmi1 shRNA
|
| Sample_geo_accession | GSM182007
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.3
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182007/suppl/GSM182007.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182008 | GPL570 |
|
Bmi1 shRNA, biological rep3
|
Human medulloblastoma DAOY cell line
|
Stable lentiviral shRNA
|
Gene expression data from DAOY cells stably expressing Bmi1 shRNA
|
| Sample_geo_accession | GSM182008
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.6
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182008/suppl/GSM182008.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182009 | GPL570 |
|
Mel18 shRNA, biological rep1
|
Human medulloblastoma DAOY cell line
|
Stable lentiviral shRNA
|
Gene expression data from DAOY cells stably expressing Mel18 shRNA
|
| Sample_geo_accession | GSM182009
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.9
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182009/suppl/GSM182009.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182010 | GPL570 |
|
Mel18 shRNA, biological rep2
|
Human medulloblastoma DAOY cell line
|
Stable lentiviral shRNA
|
Gene expression data from DAOY cells stably expressing Mel18 shRNA
|
| Sample_geo_accession | GSM182010
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.12
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182010/suppl/GSM182010.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182011 | GPL570 |
|
Mel18 shRNA, biological rep3
|
Human medulloblastoma DAOY cell line
|
Stable lentiviral shRNA
|
Gene expression data from DAOY cells stably expressing Mel18 shRNA
|
| Sample_geo_accession | GSM182011
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182011/suppl/GSM182011.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182012 | GPL570 |
|
Bmi1 Mel18 shRNA, biological rep1
|
Human medulloblastoma DAOY cell line
|
Stable lentiviral shRNA
|
Gene expression data from DAOY cells stably expressing Bmi1 and Mel18 shRNA
|
| Sample_geo_accession | GSM182012
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.18
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182012/suppl/GSM182012.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182013 | GPL570 |
|
Bmi1 Mel18 shRNA, biological rep2
|
Human medulloblastoma DAOY cell line
|
Stable lentiviral shRNA
|
Gene expression data from DAOY cells stably expressing Bmi1 and Mel18 shRNA
|
| Sample_geo_accession | GSM182013
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.21
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182013/suppl/GSM182013.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182014 | GPL570 |
|
Bmi1 Mel18 shRNA, biological rep3
|
Human medulloblastoma DAOY cell line
|
Stable lentiviral shRNA
|
Gene expression data from DAOY cells stably expressing Bmi1 and Mel18 shRNA
|
| Sample_geo_accession | GSM182014
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.24
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182014/suppl/GSM182014.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182015 | GPL570 |
|
Alk shRNA, biological rep1
|
Human medulloblastoma DAOY cell line
|
Stable lentiviral shRNA
|
Gene expression data from DAOY cells stably expressing Alk shRNA
|
| Sample_geo_accession | GSM182015
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.27
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182015/suppl/GSM182015.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182016 | GPL570 |
|
Alk shRNA, biological rep2
|
Human medulloblastoma DAOY cell line
|
Stable lentiviral shRNA
|
Gene expression data from DAOY cells stably expressing Alk shRNA
|
| Sample_geo_accession | GSM182016
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.30
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182016/suppl/GSM182016.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182017 | GPL570 |
|
Alk shRNA, biological rep3
|
Human medulloblastoma DAOY cell line
|
Stable lentiviral shRNA
|
Gene expression data from DAOY cells stably expressing Alk shRNA
|
| Sample_geo_accession | GSM182017
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.33
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182017/suppl/GSM182017.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182018 | GPL570 |
|
Wild Type, biological rep1
|
Human medulloblastoma DAOY cell line
|
Untransduced Wild Type DAOY Cells
|
Gene expression data from wild type DAOY cells
|
| Sample_geo_accession | GSM182018
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were mock transduced and 2 x 105 cells were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.36
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182018/suppl/GSM182018.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182019 | GPL570 |
|
Wild Type, biological rep2
|
Human medulloblastoma DAOY cell line
|
Untransduced Wild Type DAOY Cells
|
Gene expression data from wild type DAOY cells
|
| Sample_geo_accession | GSM182019
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were mock transduced and 2 x 105 cells were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.39
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182019/suppl/GSM182019.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
GSM182020 | GPL570 |
|
Wild Type, biological rep3
|
Human medulloblastoma DAOY cell line
|
Untransduced Wild Type DAOY Cells
|
Gene expression data from wild type DAOY cells
|
| Sample_geo_accession | GSM182020
| | Sample_status | Public on May 01 2007
| | Sample_submission_date | Apr 12 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were mock transduced and 2 x 105 cells were plated onto 60 mm dishes in triplicates and harvested 4 days later.
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)
| | Sample_hyb_protocol | The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.
| | Sample_scan_protocol | Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.42
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dmitri,,Wiederschain
| | Sample_contact_email | michaeld.jones@novartis.com
| | Sample_contact_phone | 617 871-7449
| | Sample_contact_department | Oncolology
| | Sample_contact_institute | Novartis
| | Sample_contact_address | 250 Massachusetts Avenue
| | Sample_contact_city | Cambdridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182020/suppl/GSM182020.cel.gz
| | Sample_series_id | GSE7578
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
