Search results for the GEO ID: GSE46538  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1131890 | GPL570 |
|
IN1472 siNT treated, Biological replicate1
|
non-targeting siRNA treated for 10 days
|
cell culture: grade VI GBM short term cultures
|
gene expression data from siNT treated IN1472 cells
|
| Sample_geo_accession | GSM1131890
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | May 01 2013
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.
| | Sample_growth_protocol_ch1 | short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to the manufacturers’ instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions
| | Sample_hyb_protocol | Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols
| | Sample_data_processing | Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farjana,B,Rowther
| | Sample_contact_email | fbrowther@wlv.ac.uk
| | Sample_contact_department | BRAIN TUMOUR RESEARCH LAB
| | Sample_contact_institute | University of Wolverhampton
| | Sample_contact_address | Wulfruna Street
| | Sample_contact_city | Wolverhampton
| | Sample_contact_zip/postal_code | WV1 1LY
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131890/suppl/GSM1131890_KK1_190412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131890/suppl/GSM1131890_KK1_190412.rma.chp.gz
| | Sample_series_id | GSE46538
| | Sample_data_row_count | 54675
| | |
|
GSM1131891 | GPL570 |
|
IN1472 siNT treated, Biological replicate2
|
non-targeting siRNA treated for 10 days
|
cell culture: grade VI GBM short term cultures
|
gene expression data from siNT treated IN1472 cells
|
| Sample_geo_accession | GSM1131891
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | May 01 2013
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.
| | Sample_growth_protocol_ch1 | short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to the manufacturers’ instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions
| | Sample_hyb_protocol | Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols
| | Sample_data_processing | Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farjana,B,Rowther
| | Sample_contact_email | fbrowther@wlv.ac.uk
| | Sample_contact_department | BRAIN TUMOUR RESEARCH LAB
| | Sample_contact_institute | University of Wolverhampton
| | Sample_contact_address | Wulfruna Street
| | Sample_contact_city | Wolverhampton
| | Sample_contact_zip/postal_code | WV1 1LY
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131891/suppl/GSM1131891_KK2_190412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131891/suppl/GSM1131891_KK2_190412.rma.chp.gz
| | Sample_series_id | GSE46538
| | Sample_data_row_count | 54675
| | |
|
GSM1131892 | GPL570 |
|
IN1472 siNT treated, Biological replicate3
|
non-targeting siRNA treated for 10 days
|
cell culture: grade VI GBM short term cultures
|
gene expression data from siNT treated IN1472 cells
|
| Sample_geo_accession | GSM1131892
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | May 01 2013
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.
| | Sample_growth_protocol_ch1 | short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to the manufacturers’ instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions
| | Sample_hyb_protocol | Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols
| | Sample_data_processing | Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farjana,B,Rowther
| | Sample_contact_email | fbrowther@wlv.ac.uk
| | Sample_contact_department | BRAIN TUMOUR RESEARCH LAB
| | Sample_contact_institute | University of Wolverhampton
| | Sample_contact_address | Wulfruna Street
| | Sample_contact_city | Wolverhampton
| | Sample_contact_zip/postal_code | WV1 1LY
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131892/suppl/GSM1131892_KK3_190412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131892/suppl/GSM1131892_KK3_190412.rma.chp.gz
| | Sample_series_id | GSE46538
| | Sample_data_row_count | 54675
| | |
|
GSM1131893 | GPL570 |
|
IN1472 siPD treated, Biological replicate1
|
PDE1C siRNA treated for 10 days
|
cell culture: grade VI GBM short term cultures
|
gene expression data from siPD treated IN1472 cells
|
| Sample_geo_accession | GSM1131893
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | May 01 2013
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.
| | Sample_growth_protocol_ch1 | short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to the manufacturers’ instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions
| | Sample_hyb_protocol | Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols
| | Sample_data_processing | Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farjana,B,Rowther
| | Sample_contact_email | fbrowther@wlv.ac.uk
| | Sample_contact_department | BRAIN TUMOUR RESEARCH LAB
| | Sample_contact_institute | University of Wolverhampton
| | Sample_contact_address | Wulfruna Street
| | Sample_contact_city | Wolverhampton
| | Sample_contact_zip/postal_code | WV1 1LY
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131893/suppl/GSM1131893_KK4_190412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131893/suppl/GSM1131893_KK4_190412.rma.chp.gz
| | Sample_series_id | GSE46538
| | Sample_data_row_count | 54675
| | |
|
GSM1131894 | GPL570 |
|
IN1472 siPD treated, Biological replicate2
|
PDE1C siRNA treated for 10 days
|
cell culture: grade VI GBM short term cultures
|
gene expression data from siPD treated IN1472 cells
|
| Sample_geo_accession | GSM1131894
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | May 01 2013
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.
| | Sample_growth_protocol_ch1 | short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to the manufacturers’ instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions
| | Sample_hyb_protocol | Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols
| | Sample_data_processing | Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farjana,B,Rowther
| | Sample_contact_email | fbrowther@wlv.ac.uk
| | Sample_contact_department | BRAIN TUMOUR RESEARCH LAB
| | Sample_contact_institute | University of Wolverhampton
| | Sample_contact_address | Wulfruna Street
| | Sample_contact_city | Wolverhampton
| | Sample_contact_zip/postal_code | WV1 1LY
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131894/suppl/GSM1131894_KK5_190412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131894/suppl/GSM1131894_KK5_190412.rma.chp.gz
| | Sample_series_id | GSE46538
| | Sample_data_row_count | 54675
| | |
|
GSM1131895 | GPL570 |
|
IN1472 siPD treated, Biological replicate3
|
PDE1C siRNA treated for 10 days
|
cell culture: grade VI GBM short term cultures
|
gene expression data from siPD treated IN1472 cells
|
| Sample_geo_accession | GSM1131895
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | May 01 2013
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.
| | Sample_growth_protocol_ch1 | short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to the manufacturers’ instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions
| | Sample_hyb_protocol | Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols
| | Sample_data_processing | Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farjana,B,Rowther
| | Sample_contact_email | fbrowther@wlv.ac.uk
| | Sample_contact_department | BRAIN TUMOUR RESEARCH LAB
| | Sample_contact_institute | University of Wolverhampton
| | Sample_contact_address | Wulfruna Street
| | Sample_contact_city | Wolverhampton
| | Sample_contact_zip/postal_code | WV1 1LY
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131895/suppl/GSM1131895_KK6_190412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131895/suppl/GSM1131895_KK6_190412.rma.chp.gz
| | Sample_series_id | GSE46538
| | Sample_data_row_count | 54675
| | |
|
GSM1131896 | GPL570 |
|
IN1760 siNT treated, Biological replicate1
|
non-targeting siRNA treated for 10 days
|
cell culture: grade VI GBM short term cultures
|
gene expression data from siNT treated IN1760 cells
|
| Sample_geo_accession | GSM1131896
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | May 01 2013
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.
| | Sample_growth_protocol_ch1 | short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to the manufacturers’ instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions
| | Sample_hyb_protocol | Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols
| | Sample_data_processing | Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farjana,B,Rowther
| | Sample_contact_email | fbrowther@wlv.ac.uk
| | Sample_contact_department | BRAIN TUMOUR RESEARCH LAB
| | Sample_contact_institute | University of Wolverhampton
| | Sample_contact_address | Wulfruna Street
| | Sample_contact_city | Wolverhampton
| | Sample_contact_zip/postal_code | WV1 1LY
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131896/suppl/GSM1131896_KK7_190412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131896/suppl/GSM1131896_KK7_190412.rma.chp.gz
| | Sample_series_id | GSE46538
| | Sample_data_row_count | 54675
| | |
|
GSM1131897 | GPL570 |
|
IN1760 siNT treated, Biological replicate2
|
non-targeting siRNA treated for 10 days
|
cell culture: grade VI GBM short term cultures
|
gene expression data from siNT treated IN1760 cells
|
| Sample_geo_accession | GSM1131897
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | May 01 2013
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.
| | Sample_growth_protocol_ch1 | short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to the manufacturers’ instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions
| | Sample_hyb_protocol | Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols
| | Sample_data_processing | Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farjana,B,Rowther
| | Sample_contact_email | fbrowther@wlv.ac.uk
| | Sample_contact_department | BRAIN TUMOUR RESEARCH LAB
| | Sample_contact_institute | University of Wolverhampton
| | Sample_contact_address | Wulfruna Street
| | Sample_contact_city | Wolverhampton
| | Sample_contact_zip/postal_code | WV1 1LY
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131897/suppl/GSM1131897_KK8_190412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131897/suppl/GSM1131897_KK8_190412.rma.chp.gz
| | Sample_series_id | GSE46538
| | Sample_data_row_count | 54675
| | |
|
GSM1131898 | GPL570 |
|
IN1760 siNT treated, Biological replicate3
|
non-targeting siRNA treated for 10 days
|
cell culture: grade VI GBM short term cultures
|
gene expression data from siNT treated IN1760 cells
|
| Sample_geo_accession | GSM1131898
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | May 01 2013
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.
| | Sample_growth_protocol_ch1 | short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to the manufacturers’ instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions
| | Sample_hyb_protocol | Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols
| | Sample_data_processing | Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farjana,B,Rowther
| | Sample_contact_email | fbrowther@wlv.ac.uk
| | Sample_contact_department | BRAIN TUMOUR RESEARCH LAB
| | Sample_contact_institute | University of Wolverhampton
| | Sample_contact_address | Wulfruna Street
| | Sample_contact_city | Wolverhampton
| | Sample_contact_zip/postal_code | WV1 1LY
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131898/suppl/GSM1131898_KK9_190412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131898/suppl/GSM1131898_KK9_190412.rma.chp.gz
| | Sample_series_id | GSE46538
| | Sample_data_row_count | 54675
| | |
|
GSM1131899 | GPL570 |
|
IN1760 siPD treated, Biological replicate1
|
PDE1C siRNA treated for 10 days
|
cell culture: grade VI GBM short term cultures
|
gene expression data from siPD treated IN1760 cells
|
| Sample_geo_accession | GSM1131899
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | May 01 2013
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.
| | Sample_growth_protocol_ch1 | short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to the manufacturers’ instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions
| | Sample_hyb_protocol | Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols
| | Sample_data_processing | Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farjana,B,Rowther
| | Sample_contact_email | fbrowther@wlv.ac.uk
| | Sample_contact_department | BRAIN TUMOUR RESEARCH LAB
| | Sample_contact_institute | University of Wolverhampton
| | Sample_contact_address | Wulfruna Street
| | Sample_contact_city | Wolverhampton
| | Sample_contact_zip/postal_code | WV1 1LY
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131899/suppl/GSM1131899_KK10_190412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131899/suppl/GSM1131899_KK10_190412.rma.chp.gz
| | Sample_series_id | GSE46538
| | Sample_data_row_count | 54675
| | |
|
GSM1131900 | GPL570 |
|
IN1760 siPD treated, Biological replicate2
|
PDE1C siRNA treated for 10 days
|
cell culture: grade VI GBM short term cultures
|
gene expression data from siPD treated IN1760 cells
|
| Sample_geo_accession | GSM1131900
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | May 01 2013
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.
| | Sample_growth_protocol_ch1 | short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to the manufacturers’ instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions
| | Sample_hyb_protocol | Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols
| | Sample_data_processing | Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farjana,B,Rowther
| | Sample_contact_email | fbrowther@wlv.ac.uk
| | Sample_contact_department | BRAIN TUMOUR RESEARCH LAB
| | Sample_contact_institute | University of Wolverhampton
| | Sample_contact_address | Wulfruna Street
| | Sample_contact_city | Wolverhampton
| | Sample_contact_zip/postal_code | WV1 1LY
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131900/suppl/GSM1131900_KK11_190412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131900/suppl/GSM1131900_KK11_190412.rma.chp.gz
| | Sample_series_id | GSE46538
| | Sample_data_row_count | 54675
| | |
|
GSM1131901 | GPL570 |
|
IN1760 siPD treated, Biological replicate3
|
PDE1C siRNA treated for 10 days
|
cell culture: grade VI GBM short term cultures
|
gene expression data from siPD treated IN1760 cells
|
| Sample_geo_accession | GSM1131901
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | May 01 2013
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.
| | Sample_growth_protocol_ch1 | short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Mini Kit according to the manufacturers’ instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions
| | Sample_hyb_protocol | Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols
| | Sample_data_processing | Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farjana,B,Rowther
| | Sample_contact_email | fbrowther@wlv.ac.uk
| | Sample_contact_department | BRAIN TUMOUR RESEARCH LAB
| | Sample_contact_institute | University of Wolverhampton
| | Sample_contact_address | Wulfruna Street
| | Sample_contact_city | Wolverhampton
| | Sample_contact_zip/postal_code | WV1 1LY
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131901/suppl/GSM1131901_KK12_190412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131901/suppl/GSM1131901_KK12_190412.rma.chp.gz
| | Sample_series_id | GSE46538
| | Sample_data_row_count | 54675
| | |
|
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