Search results for the GEO ID: GSE15367  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM385336 | GPL570 |
|
Null, Untreated, rep 1
|
Saos-2 osteosarcoma, p53-null, untreated
|
mutation: p53 null
treatment: untreated
cell line: Saos-2
cell type: osteosarcoma
|
Microsoft Excel program was used to merge the overlapping significant genes from the settings. Annotations from Affymetrix for significant genes were checked in NCBI public database and pathway analysis were used by Ingenuity.
|
| Sample_geo_accession | GSM385336
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Mar 23 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit (Qiagen, Sweden) according to manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin labeled cRNA was produced according to Affymetrix protocol
| | Sample_hyb_protocol | Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.
| | Sample_scan_protocol | The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix, Inc.).
| | Sample_data_processing | The results were quantified, and normalized using MAS5.0. The genes with probe set signal lower than 50 on the repeated arrays were considered as non-expression and filtered out. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency. GeneSpring software from Agilent was used for the filtration and pathway analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jeremy,,Lambert
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | CCK, R8:04
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 17176
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM385nnn/GSM385336/suppl/GSM385336.CEL.gz
| | Sample_series_id | GSE15367
| | Sample_series_id | GSE15658
| | Sample_data_row_count | 54675
| | |
|
GSM385356 | GPL570 |
|
Null, 6 hours treatment, rep 1
|
Saos-2 osteosarcoma, p53-null, 6 hours treatment
|
mutation: p53 null
treatment: 6 hours treatment with Prima
cell line: Saos-2
cell type: osteosarcoma
|
Microsoft Excel program was used to merge the overlapping significant genes from the settings. Annotations from Affymetrix for significant genes were checked in NCBI public database and pathway analysis were used by Ingenuity.
|
| Sample_geo_accession | GSM385356
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Mar 23 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit (Qiagen, Sweden) according to manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin labeled cRNA was produced according to Affymetrix protocol
| | Sample_hyb_protocol | Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.
| | Sample_scan_protocol | The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix, Inc.).
| | Sample_data_processing | The results were quantified, and normalized using MAS5.0. The genes with probe set signal lower than 50 on the repeated arrays were considered as non-expression and filtered out. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency. GeneSpring software from Agilent was used for the filtration and pathway analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jeremy,,Lambert
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | CCK, R8:04
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 17176
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM385nnn/GSM385356/suppl/GSM385356.CEL.gz
| | Sample_series_id | GSE15367
| | Sample_series_id | GSE15658
| | Sample_data_row_count | 54675
| | |
|
GSM385359 | GPL570 |
|
Null, Untreated, rep 2
|
Saos-2 osteosarcoma, p53-null, untreated
|
mutation: p53 null
treatment: untreated
cell line: Saos-2
cell type: osteosarcoma
|
Microsoft Excel program was used to merge the overlapping significant genes from the settings. Annotations from Affymetrix for significant genes were checked in NCBI public database and pathway analysis were used by Ingenuity.
|
| Sample_geo_accession | GSM385359
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Mar 23 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit (Qiagen, Sweden) according to manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin labeled cRNA was produced according to Affymetrix protocol
| | Sample_hyb_protocol | Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.
| | Sample_scan_protocol | The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix, Inc.).
| | Sample_data_processing | The results were quantified, and normalized using MAS5.0. The genes with probe set signal lower than 50 on the repeated arrays were considered as non-expression and filtered out. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency. GeneSpring software from Agilent was used for the filtration and pathway analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jeremy,,Lambert
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | CCK, R8:04
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 17176
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM385nnn/GSM385359/suppl/GSM385359.CEL.gz
| | Sample_series_id | GSE15367
| | Sample_series_id | GSE15658
| | Sample_data_row_count | 54675
| | |
|
GSM385362 | GPL570 |
|
Null, 6 hours treatment, rep 2
|
Saos-2 osteosarcoma, p53-null, 6 hours treatment
|
mutation: p53 null
treatment: 6 hours treatment with Prima
cell line: Saos-2
cell type: osteosarcoma
|
Microsoft Excel program was used to merge the overlapping significant genes from the settings. Annotations from Affymetrix for significant genes were checked in NCBI public database and pathway analysis were used by Ingenuity.
|
| Sample_geo_accession | GSM385362
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Mar 23 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit (Qiagen, Sweden) according to manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin labeled cRNA was produced according to Affymetrix protocol
| | Sample_hyb_protocol | Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.
| | Sample_scan_protocol | The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix, Inc.).
| | Sample_data_processing | The results were quantified, and normalized using MAS5.0. The genes with probe set signal lower than 50 on the repeated arrays were considered as non-expression and filtered out. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency. GeneSpring software from Agilent was used for the filtration and pathway analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jeremy,,Lambert
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | CCK, R8:04
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 17176
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM385nnn/GSM385362/suppl/GSM385362.CEL.gz
| | Sample_series_id | GSE15367
| | Sample_series_id | GSE15658
| | Sample_data_row_count | 54675
| | |
|
GSM385363 | GPL570 |
|
Null, 12 hours treatment, rep 1
|
Saos-2 osteosarcoma, p53-null, 12 hours treatment
|
mutation: p53 null
treatment: 12 hours treatment with Prima
cell line: Saos-2
cell type: osteosarcoma
|
Microsoft Excel program was used to merge the overlapping significant genes from the settings. Annotations from Affymetrix for significant genes were checked in NCBI public database and pathway analysis were used by Ingenuity.
|
| Sample_geo_accession | GSM385363
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Mar 23 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit (Qiagen, Sweden) according to manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin labeled cRNA was produced according to Affymetrix protocol
| | Sample_hyb_protocol | Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.
| | Sample_scan_protocol | The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix, Inc.).
| | Sample_data_processing | The results were quantified, and normalized using MAS5.0. The genes with probe set signal lower than 50 on the repeated arrays were considered as non-expression and filtered out. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency. GeneSpring software from Agilent was used for the filtration and pathway analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jeremy,,Lambert
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | CCK, R8:04
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 17176
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM385nnn/GSM385363/suppl/GSM385363.CEL.gz
| | Sample_series_id | GSE15367
| | Sample_series_id | GSE15658
| | Sample_data_row_count | 54675
| | |
|
GSM385390 | GPL570 |
|
Null, Untreated, rep 3
|
Saos-2 osteosarcoma, p53-null, untreated
|
mutation: p53 null
treatment: untreated
cell line: Saos-2
cell type: osteosarcoma
|
Microsoft Excel program was used to merge the overlapping significant genes from the settings. Annotations from Affymetrix for significant genes were checked in NCBI public database and pathway analysis were used by Ingenuity.
|
| Sample_geo_accession | GSM385390
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Mar 23 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit (Qiagen, Sweden) according to manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin labeled cRNA was produced according to Affymetrix protocol
| | Sample_hyb_protocol | Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.
| | Sample_scan_protocol | The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix, Inc.).
| | Sample_data_processing | The results were quantified, and normalized using MAS5.0. The genes with probe set signal lower than 50 on the repeated arrays were considered as non-expression and filtered out. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency. GeneSpring software from Agilent was used for the filtration and pathway analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jeremy,,Lambert
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | CCK, R8:04
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 17176
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM385nnn/GSM385390/suppl/GSM385390.CEL.gz
| | Sample_series_id | GSE15367
| | Sample_series_id | GSE15658
| | Sample_data_row_count | 54675
| | |
|
GSM385391 | GPL570 |
|
Null, 6 hours treatment, rep 3
|
Saos-2 osteosarcoma, p53-null, 6 hours treatment
|
mutation: p53 null
treatment: 6 hours treatment with Prima
cell line: Saos-2
cell type: osteosarcoma
|
Microsoft Excel program was used to merge the overlapping significant genes from the settings. Annotations from Affymetrix for significant genes were checked in NCBI public database and pathway analysis were used by Ingenuity.
|
| Sample_geo_accession | GSM385391
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Mar 23 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit (Qiagen, Sweden) according to manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin labeled cRNA was produced according to Affymetrix protocol
| | Sample_hyb_protocol | Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.
| | Sample_scan_protocol | The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix, Inc.).
| | Sample_data_processing | The results were quantified, and normalized using MAS5.0. The genes with probe set signal lower than 50 on the repeated arrays were considered as non-expression and filtered out. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency. GeneSpring software from Agilent was used for the filtration and pathway analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jeremy,,Lambert
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | CCK, R8:04
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 17176
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM385nnn/GSM385391/suppl/GSM385391.CEL.gz
| | Sample_series_id | GSE15367
| | Sample_series_id | GSE15658
| | Sample_data_row_count | 54675
| | |
|
GSM385392 | GPL570 |
|
Null, 12 hours treatment, rep 3
|
Saos-2 osteosarcoma, p53-null, 12 hours treatment
|
mutation: p53 null
treatment: 12 hours treatment with Prima
cell line: Saos-2
cell type: osteosarcoma
|
Microsoft Excel program was used to merge the overlapping significant genes from the settings. Annotations from Affymetrix for significant genes were checked in NCBI public database and pathway analysis were used by Ingenuity.
|
| Sample_geo_accession | GSM385392
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Mar 23 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit (Qiagen, Sweden) according to manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin labeled cRNA was produced according to Affymetrix protocol
| | Sample_hyb_protocol | Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.
| | Sample_scan_protocol | The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix, Inc.).
| | Sample_data_processing | The results were quantified, and normalized using MAS5.0. The genes with probe set signal lower than 50 on the repeated arrays were considered as non-expression and filtered out. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency. GeneSpring software from Agilent was used for the filtration and pathway analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jeremy,,Lambert
| | Sample_contact_institute | Karolinska Institutet
| | Sample_contact_address | CCK, R8:04
| | Sample_contact_city | Stockholm
| | Sample_contact_zip/postal_code | 17176
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM385nnn/GSM385392/suppl/GSM385392.CEL.gz
| | Sample_series_id | GSE15367
| | Sample_series_id | GSE15658
| | Sample_data_row_count | 54675
| | |
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