Search results for the GEO ID: GSE39218  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM958279 | GPL570 |
|
t=24,SHC002,IMR32
|
IMR32
|
cell line: IMR32
cell type: Neuroblastoma cell line
viral transduction status: with control virus
time: 24 hrs
|
|
| Sample_geo_accession | GSM958279
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Jul 10 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IMR32 were transduced with pLenti-virus particles with control (SHC002, Sigma) or MYCN (TRCN0000020696, Sigma) shRNA
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958279/suppl/GSM958279_NB607.CEL.gz
| | Sample_series_id | GSE39218
| | Sample_data_row_count | 54675
| | |
|
GSM958280 | GPL570 |
|
t=48,SHC002,IMR32
|
IMR32
|
cell line: IMR32
cell type: Neuroblastoma cell line
viral transduction status: with control virus
time: 48 hrs
|
|
| Sample_geo_accession | GSM958280
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Jul 10 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IMR32 were transduced with pLenti-virus particles with control (SHC002, Sigma) or MYCN (TRCN0000020696, Sigma) shRNA
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958280/suppl/GSM958280_NB608.CEL.gz
| | Sample_series_id | GSE39218
| | Sample_data_row_count | 54675
| | |
|
GSM958281 | GPL570 |
|
t=72,SHC002,IMR32
|
IMR32
|
cell line: IMR32
cell type: Neuroblastoma cell line
viral transduction status: with control virus
time: 72 hrs
|
|
| Sample_geo_accession | GSM958281
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Jul 10 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IMR32 were transduced with pLenti-virus particles with control (SHC002, Sigma) or MYCN (TRCN0000020696, Sigma) shRNA
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958281/suppl/GSM958281_NB609.CEL.gz
| | Sample_series_id | GSE39218
| | Sample_data_row_count | 54675
| | |
|
GSM958282 | GPL570 |
|
t=0, no virus, rep 1
|
IMR32
|
cell line: IMR32
cell type: Neuroblastoma cell line
viral transduction status: control
time: 0 hrs
|
|
| Sample_geo_accession | GSM958282
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Jul 10 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IMR32 were transduced with pLenti-virus particles with control (SHC002, Sigma) or MYCN (TRCN0000020696, Sigma) shRNA
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958282/suppl/GSM958282_NB610.CEL.gz
| | Sample_series_id | GSE39218
| | Sample_data_row_count | 54675
| | |
|
GSM958283 | GPL570 |
|
t=24, shMYCN#3, A
|
IMR32
|
cell line: IMR32
cell type: Neuroblastoma cell line
viral transduction status: with shMYCN virus
time: 24 hrs
|
|
| Sample_geo_accession | GSM958283
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Jul 10 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IMR32 were transduced with pLenti-virus particles with control (SHC002, Sigma) or MYCN (TRCN0000020696, Sigma) shRNA
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958283/suppl/GSM958283_NB611.CEL.gz
| | Sample_series_id | GSE39218
| | Sample_data_row_count | 54675
| | |
|
GSM958284 | GPL570 |
|
t=48, shMYCN#3, A
|
IMR32
|
cell line: IMR32
cell type: Neuroblastoma cell line
viral transduction status: with shMYCN virus
time: 48 hrs
|
|
| Sample_geo_accession | GSM958284
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Jul 10 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IMR32 were transduced with pLenti-virus particles with control (SHC002, Sigma) or MYCN (TRCN0000020696, Sigma) shRNA
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958284/suppl/GSM958284_NB612.CEL.gz
| | Sample_series_id | GSE39218
| | Sample_data_row_count | 54675
| | |
|
GSM958285 | GPL570 |
|
t=72, shMYCN#3, A
|
IMR32
|
cell line: IMR32
cell type: Neuroblastoma cell line
viral transduction status: with shMYCN virus
time: 72 hrs
|
|
| Sample_geo_accession | GSM958285
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Jul 10 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IMR32 were transduced with pLenti-virus particles with control (SHC002, Sigma) or MYCN (TRCN0000020696, Sigma) shRNA
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958285/suppl/GSM958285_NB613.CEL.gz
| | Sample_series_id | GSE39218
| | Sample_data_row_count | 54675
| | |
|
GSM958286 | GPL570 |
|
t=0, no virus, rep 2
|
IMR32
|
cell line: IMR32
cell type: Neuroblastoma cell line
viral transduction status: control
time: 0 hrs
|
|
| Sample_geo_accession | GSM958286
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Jul 10 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IMR32 were transduced with pLenti-virus particles with control (SHC002, Sigma) or MYCN (TRCN0000020696, Sigma) shRNA
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958286/suppl/GSM958286_NB614.CEL.gz
| | Sample_series_id | GSE39218
| | Sample_data_row_count | 54675
| | |
|
GSM958287 | GPL570 |
|
t=24, shMYCN#3, B
|
IMR32
|
cell line: IMR32
cell type: Neuroblastoma cell line
viral transduction status: with shMYCN virus (duplo)
time: 24 hrs
|
|
| Sample_geo_accession | GSM958287
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Jul 10 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IMR32 were transduced with pLenti-virus particles with control (SHC002, Sigma) or MYCN (TRCN0000020696, Sigma) shRNA
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958287/suppl/GSM958287_NB615.CEL.gz
| | Sample_series_id | GSE39218
| | Sample_data_row_count | 54675
| | |
|
GSM958288 | GPL570 |
|
t=48, shMYCN#3, B
|
IMR32
|
cell line: IMR32
cell type: Neuroblastoma cell line
viral transduction status: with shMYCN virus (duplo)
time: 48 hrs
|
|
| Sample_geo_accession | GSM958288
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Jul 10 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IMR32 were transduced with pLenti-virus particles with control (SHC002, Sigma) or MYCN (TRCN0000020696, Sigma) shRNA
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958288/suppl/GSM958288_NB616.CEL.gz
| | Sample_series_id | GSE39218
| | Sample_data_row_count | 54675
| | |
|
GSM958289 | GPL570 |
|
t=72, shMYCN#3, B
|
IMR32
|
cell line: IMR32
cell type: Neuroblastoma cell line
viral transduction status: with shMYCN virus (duplo)
time: 72 hrs
|
|
| Sample_geo_accession | GSM958289
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Jul 10 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IMR32 were transduced with pLenti-virus particles with control (SHC002, Sigma) or MYCN (TRCN0000020696, Sigma) shRNA
| | Sample_growth_protocol_ch1 | IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958289/suppl/GSM958289_NB617.CEL.gz
| | Sample_series_id | GSE39218
| | Sample_data_row_count | 54675
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