Search results for the GEO ID: GSE22139  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM550686 | GPL570 |
|
medulloblastoma, wt, rep1
|
medulloblastoma, wt
|
cell line: DAOY
cell type: medulloblastoma
genetic modification: none (wildtype)
|
Gene expression data.
|
| Sample_geo_accession | GSM550686
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550686/suppl/GSM550686.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550687 | GPL570 |
|
medulloblastoma, wt, rep2
|
medulloblastoma, wt
|
cell line: DAOY
cell type: medulloblastoma
genetic modification: none (wildtype)
|
Gene expression data.
|
| Sample_geo_accession | GSM550687
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550687/suppl/GSM550687.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550688 | GPL570 |
|
medulloblastoma, wt, rep3
|
medulloblastoma, wt
|
cell line: DAOY
cell type: medulloblastoma
genetic modification: none (wildtype)
|
Gene expression data.
|
| Sample_geo_accession | GSM550688
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550688/suppl/GSM550688.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550689 | GPL570 |
|
medulloblastoma, M2, rep1
|
medulloblastoma, M2
|
cell line: DAOY M2.1
cell type: medulloblastoma
genetic modification: pMYCEGFP vector-transfected
|
Gene expression data.
|
| Sample_geo_accession | GSM550689
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550689/suppl/GSM550689.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550690 | GPL570 |
|
medulloblastoma, M2, rep2
|
medulloblastoma, M2
|
cell line: DAOY M2.1
cell type: medulloblastoma
genetic modification: pMYCEGFP vector-transfected
|
Gene expression data.
|
| Sample_geo_accession | GSM550690
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550690/suppl/GSM550690.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550691 | GPL570 |
|
medulloblastoma, M2, rep3
|
medulloblastoma, M2
|
cell line: DAOY M2.1
cell type: medulloblastoma
genetic modification: pMYCEGFP vector-transfected
|
Gene expression data.
|
| Sample_geo_accession | GSM550691
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550691/suppl/GSM550691.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550692 | GPL570 |
|
medulloblastoma, V11, rep1
|
medulloblastoma, V11
|
cell line: DAOY V11
cell type: medulloblastoma
genetic modification: pEGFP vector-transfected
|
Gene expression data.
|
| Sample_geo_accession | GSM550692
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550692/suppl/GSM550692.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550693 | GPL570 |
|
medulloblastoma, V11, rep2
|
medulloblastoma, V11
|
cell line: DAOY V11
cell type: medulloblastoma
genetic modification: pEGFP vector-transfected
|
Gene expression data.
|
| Sample_geo_accession | GSM550693
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550693/suppl/GSM550693.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550694 | GPL570 |
|
medulloblastoma, V11, rep3
|
medulloblastoma, V11
|
cell line: DAOY V11
cell type: medulloblastoma
genetic modification: pEGFP vector-transfected
|
Gene expression data.
|
| Sample_geo_accession | GSM550694
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550694/suppl/GSM550694.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550695 | GPL570 |
|
medulloblastoma, M14, rep1
|
medulloblastoma, M14
|
cell line: DAOY M14
cell type: medulloblastoma
genetic modification: pMYCEGFP vector-transfected
|
Gene expression data.
|
| Sample_geo_accession | GSM550695
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550695/suppl/GSM550695.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550696 | GPL570 |
|
medulloblastoma, M14, rep2
|
medulloblastoma, M14
|
cell line: DAOY M14
cell type: medulloblastoma
genetic modification: pMYCEGFP vector-transfected
|
Gene expression data.
|
| Sample_geo_accession | GSM550696
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550696/suppl/GSM550696.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550697 | GPL570 |
|
medulloblastoma, M14, rep3
|
medulloblastoma, M14
|
cell line: DAOY M14
cell type: medulloblastoma
genetic modification: pMYCEGFP vector-transfected
|
Gene expression data.
|
| Sample_geo_accession | GSM550697
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550697/suppl/GSM550697.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550698 | GPL570 |
|
medulloblastoma, M2_scrambled, rep1
|
medulloblastoma, M2, scrambled
|
cell line: DAOY M2.1
cell type: medulloblastoma
genetic modification: siRNA scrambled
|
Gene expression data.
|
| Sample_geo_accession | GSM550698
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550698/suppl/GSM550698.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550699 | GPL570 |
|
medulloblastoma, M2_scrambled, rep2
|
medulloblastoma, M2, scrambled
|
cell line: DAOY M2.1
cell type: medulloblastoma
genetic modification: siRNA scrambled
|
Gene expression data.
|
| Sample_geo_accession | GSM550699
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550699/suppl/GSM550699.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550700 | GPL570 |
|
medulloblastoma, M2_scrambled, rep3
|
medulloblastoma, M2, scrambled
|
cell line: DAOY M2.1
cell type: medulloblastoma
genetic modification: siRNA scrambled
|
Gene expression data.
|
| Sample_geo_accession | GSM550700
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550700/suppl/GSM550700.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550701 | GPL570 |
|
medulloblastoma, M2_cMYC_silenced, rep1
|
medulloblastoma, M2, cMYC silenced
|
cell line: DAOY M2.1
cell type: medulloblastoma
genetic modification: siRNA cMYC silenced
|
Gene expression data.
|
| Sample_geo_accession | GSM550701
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550701/suppl/GSM550701.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550702 | GPL570 |
|
medulloblastoma, M2_cMYC_silenced, rep2
|
medulloblastoma, M2, cMYC silenced
|
cell line: DAOY M2.1
cell type: medulloblastoma
genetic modification: siRNA cMYC silenced
|
Gene expression data.
|
| Sample_geo_accession | GSM550702
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550702/suppl/GSM550702.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
| | |
|
GSM550703 | GPL570 |
|
medulloblastoma, M2_cMYC_silenced, rep3
|
medulloblastoma, M2, cMYC silenced
|
cell line: DAOY M2.1
cell type: medulloblastoma
genetic modification: siRNA cMYC silenced
|
Gene expression data.
|
| Sample_geo_accession | GSM550703
| | Sample_status | Public on May 16 2011
| | Sample_submission_date | Jun 04 2010
| | Sample_last_update_date | May 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.
| | Sample_growth_protocol_ch1 | DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).
| | Sample_hyb_protocol | Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.
| | Sample_data_processing | Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stefan,,Zoller
| | Sample_contact_email | szoller@env.ethz.ch
| | Sample_contact_department | Genetic Diversity Centre
| | Sample_contact_institute | ETH Zurich
| | Sample_contact_address | Universitatstrasse 16
| | Sample_contact_city | Zurich
| | Sample_contact_zip/postal_code | 8092
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM550nnn/GSM550703/suppl/GSM550703.CEL.gz
| | Sample_series_id | GSE22139
| | Sample_data_row_count | 54675
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