Search results for the GEO ID: GSE32374  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM801462 | GPL570 |
|
pediatric GBM tumor sample (PBGM_ID00000)
|
patient tumor sample
|
gender: M
age at diagnosis (years): 5
disease state: pediatric GBM tumor
|
pediatric GBM tumor sample
GBM_ID00000_1.CEL
|
| Sample_geo_accession | GSM801462
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801462/suppl/GSM801462.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801463 | GPL570 |
|
pediatric GBM tumor sample (PBGM_ID00057)
|
patient tumor sample
|
gender: F
age at diagnosis (years): 13
disease state: pediatric GBM tumor
|
pediatric GBM tumor sample
GBM_ID00057_1.CEL
|
| Sample_geo_accession | GSM801463
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801463/suppl/GSM801463.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801464 | GPL570 |
|
pediatric GBM tumor sample (PBGM_ID00089)
|
patient tumor sample
|
gender: M
age at diagnosis (years): 5
disease state: pediatric GBM tumor
|
pediatric GBM tumor sample
GBM_ID00089_1.CEL
|
| Sample_geo_accession | GSM801464
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801464/suppl/GSM801464.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801465 | GPL570 |
|
pediatric GBM tumor sample (PBGM_ID00098)
|
patient tumor sample
|
gender: F
age at diagnosis (years): 7
disease state: pediatric GBM tumor
|
pediatric GBM tumor sample
GBM_ID00098_1.CEL
|
| Sample_geo_accession | GSM801465
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801465/suppl/GSM801465.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801466 | GPL570 |
|
pediatric GBM tumor sample (PBGM_ID00271)
|
patient tumor sample
|
gender: M
age at diagnosis (years): 8
disease state: pediatric GBM tumor
|
pediatric GBM tumor sample
GBM_ID00271_1.CEL
|
| Sample_geo_accession | GSM801466
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801466/suppl/GSM801466.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801467 | GPL570 |
|
pediatric GBM tumor sample (PBGM_ID00281)
|
patient tumor sample
|
gender: F
age at diagnosis (years): 16
disease state: pediatric GBM tumor
|
pediatric GBM tumor sample
GBM_ID00281_1.CEL
|
| Sample_geo_accession | GSM801467
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801467/suppl/GSM801467.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801468 | GPL570 |
|
pediatric GBM tumor sample (PBGM_ID00309)
|
patient tumor sample
|
gender: F
age at diagnosis (years): 5
disease state: pediatric GBM tumor
|
pediatric GBM tumor sample
GBM_ID00309_1.CEL
|
| Sample_geo_accession | GSM801468
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801468/suppl/GSM801468.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801469 | GPL570 |
|
pediatric GBM tumor sample (PBGM_ID00391)
|
patient tumor sample
|
gender: F
age at diagnosis (years): 3
disease state: pediatric GBM tumor
|
pediatric GBM tumor sample
GBM_ID00391_1.CEL
|
| Sample_geo_accession | GSM801469
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801469/suppl/GSM801469.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801470 | GPL570 |
|
pediatric GBM tumor sample (PBGM_ID00434)
|
patient tumor sample
|
gender: F
age at diagnosis (years): 12
disease state: pediatric GBM tumor
|
pediatric GBM tumor sample
GBM_ID00434_1.CEL
|
| Sample_geo_accession | GSM801470
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801470/suppl/GSM801470.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801471 | GPL570 |
|
pediatric GBM tumor sample (PBGM_ID00637)
|
patient tumor sample
|
gender: F
age at diagnosis (years): 4
disease state: pediatric GBM tumor
|
pediatric GBM tumor sample
GBM_ID00637_1.CEL
|
| Sample_geo_accession | GSM801471
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801471/suppl/GSM801471.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801472 | GPL570 |
|
pediatric GBM tumor sample (PBGM_ID00668)
|
patient tumor sample
|
gender: F
age at diagnosis (years): 4
disease state: pediatric GBM tumor
|
pediatric GBM tumor sample
GBM_ID00668_1.CEL
|
| Sample_geo_accession | GSM801472
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801472/suppl/GSM801472.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801473 | GPL570 |
|
pediatric GBM tumor sample (PBGM_ID00678)
|
patient tumor sample
|
gender: F
age at diagnosis (years): 10
disease state: pediatric GBM tumor
|
pediatric GBM tumor sample
GBM_ID00678_1.CEL
|
| Sample_geo_accession | GSM801473
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801473/suppl/GSM801473.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801474 | GPL570 |
|
adult GBM tumor sample (ABGM_xB00010)
|
patient tumor sample
|
gender: M
age at diagnosis (years): 46
disease state: adult GBM tumor
|
adult GBM tumor sample
GBM_xB00010_1.CEL
|
| Sample_geo_accession | GSM801474
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801474/suppl/GSM801474.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801475 | GPL570 |
|
adult GBM tumor sample (ABGM_xB00011)
|
patient tumor sample
|
gender: F
age at diagnosis (years): 46
disease state: adult GBM tumor
|
adult GBM tumor sample
GBM_xB00011_1.CEL
|
| Sample_geo_accession | GSM801475
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801475/suppl/GSM801475.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801476 | GPL570 |
|
adult GBM tumor sample (ABGM_xB00012)
|
patient tumor sample
|
gender: M
age at diagnosis (years): 38
disease state: adult GBM tumor
|
adult GBM tumor sample
GBM_xB00012_1.CEL
|
| Sample_geo_accession | GSM801476
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801476/suppl/GSM801476.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801477 | GPL570 |
|
adult GBM tumor sample (ABGM_xB00017)
|
patient tumor sample
|
gender: M
age at diagnosis (years): 73
disease state: adult GBM tumor
|
adult GBM tumor sample
GBM_xB00017_1.CEL
|
| Sample_geo_accession | GSM801477
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801477/suppl/GSM801477.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801478 | GPL570 |
|
adult GBM tumor sample (ABGM_xB00056)
|
patient tumor sample
|
gender: M
age at diagnosis (years): 71
disease state: adult GBM tumor
|
adult GBM tumor sample
GBM_xB00056_1.CEL
|
| Sample_geo_accession | GSM801478
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801478/suppl/GSM801478.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801479 | GPL570 |
|
adult GBM tumor sample (ABGM_xB00057)
|
patient tumor sample
|
gender: F
age at diagnosis (years): 50
disease state: adult GBM tumor
|
adult GBM tumor sample
GBM_xB00057_1.CEL
|
| Sample_geo_accession | GSM801479
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801479/suppl/GSM801479.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801480 | GPL570 |
|
congenital GBM tumor sample (CBGM_ID00280)
|
patient tumor sample
|
gender: M
age at diagnosis (years): 0.167
disease state: congenital GBM tumor
|
congenital GBM tumor sample
GBMI_ID00280_1.CEL
|
| Sample_geo_accession | GSM801480
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801480/suppl/GSM801480.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801481 | GPL570 |
|
congenital GBM tumor sample (CBGM_ID00531)
|
patient tumor sample
|
gender: F
age at diagnosis (years): 0.25
disease state: congenital GBM tumor
|
congenital GBM tumor sample
GBMI_ID00531_1.CEL
|
| Sample_geo_accession | GSM801481
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801481/suppl/GSM801481.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
|
GSM801482 | GPL570 |
|
congenital GBM tumor sample (CBGM_ID00692)
|
patient tumor sample
|
gender: M
age at diagnosis (years): 0.21
disease state: congenital GBM tumor
|
congenital GBM tumor sample
GBMI_ID00692_1.CEL
|
| Sample_geo_accession | GSM801482
| | Sample_status | Public on May 21 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | May 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | all samples were collected at time of surgery
| | Sample_growth_protocol_ch1 | n/a
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801482/suppl/GSM801482.CEL.gz
| | Sample_series_id | GSE32374
| | Sample_data_row_count | 54675
| | |
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