Search results for the GEO ID: GSE35493  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM869617 | GPL570 |
|
AT/RT, ID03161
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID03161
|
| Sample_geo_accession | GSM869617
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869617/suppl/GSM869617.CEL.gz
| | Sample_relation | Reanalysis of: GSM692982
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869618 | GPL570 |
|
AT/RT, ID00003
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00003
|
| Sample_geo_accession | GSM869618
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869618/suppl/GSM869618.CEL.gz
| | Sample_relation | Reanalysis of: GSM692983
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869619 | GPL570 |
|
AT/RT, ID00119
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00119
|
| Sample_geo_accession | GSM869619
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869619/suppl/GSM869619.CEL.gz
| | Sample_relation | Reanalysis of: GSM692984
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869620 | GPL570 |
|
AT/RT, ID00343
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00343
|
| Sample_geo_accession | GSM869620
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869620/suppl/GSM869620.CEL.gz
| | Sample_relation | Reanalysis of: GSM692985
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869621 | GPL570 |
|
AT/RT, ID00370
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00370
|
| Sample_geo_accession | GSM869621
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869621/suppl/GSM869621.CEL.gz
| | Sample_relation | Reanalysis of: GSM692986
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869622 | GPL570 |
|
AT/RT, ID00404
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00404
|
| Sample_geo_accession | GSM869622
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869622/suppl/GSM869622.CEL.gz
| | Sample_relation | Reanalysis of: GSM692987
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869623 | GPL570 |
|
AT/RT, ID00413
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00413
|
| Sample_geo_accession | GSM869623
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869623/suppl/GSM869623.CEL.gz
| | Sample_relation | Reanalysis of: GSM692988
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869624 | GPL570 |
|
AT/RT, ID00504
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00504
|
| Sample_geo_accession | GSM869624
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869624/suppl/GSM869624.CEL.gz
| | Sample_relation | Reanalysis of: GSM692989
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869625 | GPL570 |
|
AT/RT, ID00514
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00514
|
| Sample_geo_accession | GSM869625
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869625/suppl/GSM869625.CEL.gz
| | Sample_relation | Reanalysis of: GSM692990
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869626 | GPL570 |
|
AT/RT, ID00515
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00515
|
| Sample_geo_accession | GSM869626
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869626/suppl/GSM869626.CEL.gz
| | Sample_relation | Reanalysis of: GSM692991
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869627 | GPL570 |
|
AT/RT, ID00517
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00517
|
| Sample_geo_accession | GSM869627
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869627/suppl/GSM869627.CEL.gz
| | Sample_relation | Reanalysis of: GSM692992
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869628 | GPL570 |
|
AT/RT, ID00605
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00605
|
| Sample_geo_accession | GSM869628
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869628/suppl/GSM869628.CEL.gz
| | Sample_relation | Reanalysis of: GSM692993
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869629 | GPL570 |
|
AT/RT, ID00663
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00663
|
| Sample_geo_accession | GSM869629
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869629/suppl/GSM869629.CEL.gz
| | Sample_relation | Reanalysis of: GSM692994
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869630 | GPL570 |
|
AT/RT, ID00687
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00687
|
| Sample_geo_accession | GSM869630
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869630/suppl/GSM869630.CEL.gz
| | Sample_relation | Reanalysis of: GSM692995
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869631 | GPL570 |
|
AT/RT, ID00737
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID00737
|
| Sample_geo_accession | GSM869631
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869631/suppl/GSM869631.CEL.gz
| | Sample_relation | Reanalysis of: GSM692996
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869632 | GPL570 |
|
AT/RT, ID90004
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID90004
|
| Sample_geo_accession | GSM869632
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869632/suppl/GSM869632.CEL.gz
| | Sample_relation | Reanalysis of: GSM692997
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869633 | GPL570 |
|
AT/RT, ID90005
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID90005
|
| Sample_geo_accession | GSM869633
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869633/suppl/GSM869633.CEL.gz
| | Sample_relation | Reanalysis of: GSM692998
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869634 | GPL570 |
|
AT/RT, ID90007
|
brain tumor, AT/RT
|
tissue: atypical teratoid / rhabdoid tumor
|
ID90007
|
| Sample_geo_accession | GSM869634
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869634/suppl/GSM869634.CEL.gz
| | Sample_relation | Reanalysis of: GSM692999
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869667 | GPL570 |
|
GBM, ID00000
|
brain tumor, glioblastoma
|
tissue: glioblastoma
|
ID00000
|
| Sample_geo_accession | GSM869667
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869667/suppl/GSM869667.CEL.gz
| | Sample_relation | Reanalysis of: GSM824275
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869668 | GPL570 |
|
GBM, ID00057
|
brain tumor, glioblastoma
|
tissue: glioblastoma
|
ID00057
|
| Sample_geo_accession | GSM869668
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869668/suppl/GSM869668.CEL.gz
| | Sample_relation | Reanalysis of: GSM824286
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869669 | GPL570 |
|
GBM, ID00089
|
brain tumor, glioblastoma
|
tissue: glioblastoma
|
ID00089
|
| Sample_geo_accession | GSM869669
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869669/suppl/GSM869669.CEL.gz
| | Sample_relation | Reanalysis of: GSM824290
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869670 | GPL570 |
|
GBM, ID00098
|
brain tumor, glioblastoma
|
tissue: glioblastoma
|
ID00098
|
| Sample_geo_accession | GSM869670
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869670/suppl/GSM869670.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869671 | GPL570 |
|
GBM, ID00271
|
brain tumor, glioblastoma
|
tissue: glioblastoma
|
ID00271
|
| Sample_geo_accession | GSM869671
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869671/suppl/GSM869671.CEL.gz
| | Sample_relation | Reanalysis of: GSM824277
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869672 | GPL570 |
|
GBM, ID00281
|
brain tumor, glioblastoma
|
tissue: glioblastoma
|
ID00281
|
| Sample_geo_accession | GSM869672
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869672/suppl/GSM869672.CEL.gz
| | Sample_relation | Reanalysis of: GSM824279
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869673 | GPL570 |
|
GBM, ID00309
|
brain tumor, glioblastoma
|
tissue: glioblastoma
|
ID00309
|
| Sample_geo_accession | GSM869673
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869673/suppl/GSM869673.CEL.gz
| | Sample_relation | Reanalysis of: GSM824280
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869674 | GPL570 |
|
GBM, ID00391
|
brain tumor, glioblastoma
|
tissue: glioblastoma
|
ID00391
|
| Sample_geo_accession | GSM869674
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869674/suppl/GSM869674.CEL.gz
| | Sample_relation | Reanalysis of: GSM824281
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869675 | GPL570 |
|
GBM, ID00434
|
brain tumor, glioblastoma
|
tissue: glioblastoma
|
ID00434
|
| Sample_geo_accession | GSM869675
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869675/suppl/GSM869675.CEL.gz
| | Sample_relation | Reanalysis of: GSM824282
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869676 | GPL570 |
|
GBM, ID00637
|
brain tumor, glioblastoma
|
tissue: glioblastoma
|
ID00637
|
| Sample_geo_accession | GSM869676
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869676/suppl/GSM869676.CEL.gz
| | Sample_relation | Reanalysis of: GSM824287
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869678 | GPL570 |
|
GBM, ID00668
|
brain tumor, glioblastoma
|
tissue: glioblastoma
|
ID00668
|
| Sample_geo_accession | GSM869678
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869678/suppl/GSM869678.CEL.gz
| | Sample_relation | Reanalysis of: GSM824288
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869679 | GPL570 |
|
GBM, ID00678
|
brain tumor, glioblastoma
|
tissue: glioblastoma
|
ID00678
|
| Sample_geo_accession | GSM869679
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869679/suppl/GSM869679.CEL.gz
| | Sample_relation | Reanalysis of: GSM824289
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869683 | GPL570 |
|
MED, ID00231
|
brain tumor, medulloblastoma, large-cell
|
tissue: medulloblastoma, large-cell
|
ID00231
|
| Sample_geo_accession | GSM869683
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869683/suppl/GSM869683.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869684 | GPL570 |
|
MED, ID00241
|
brain tumor, medulloblastoma, large-cell
|
tissue: medulloblastoma, large-cell
|
ID00241
|
| Sample_geo_accession | GSM869684
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869684/suppl/GSM869684.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869685 | GPL570 |
|
MED, ID00401
|
brain tumor, medulloblastoma, large-cell
|
tissue: medulloblastoma, large-cell
|
ID00401
|
| Sample_geo_accession | GSM869685
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869685/suppl/GSM869685.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869686 | GPL570 |
|
MED, ID00613
|
brain tumor, medulloblastoma, large-cell
|
tissue: medulloblastoma, large-cell
|
ID00613
|
| Sample_geo_accession | GSM869686
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869686/suppl/GSM869686.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869688 | GPL570 |
|
MED, ID00186
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
ID00186
|
| Sample_geo_accession | GSM869688
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869688/suppl/GSM869688.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869689 | GPL570 |
|
MED, ID00254
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
ID00254
|
| Sample_geo_accession | GSM869689
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869689/suppl/GSM869689.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869690 | GPL570 |
|
MED, ID00258
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
ID00258
|
| Sample_geo_accession | GSM869690
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869690/suppl/GSM869690.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869691 | GPL570 |
|
MED, ID00262
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
ID00262
|
| Sample_geo_accession | GSM869691
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869691/suppl/GSM869691.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869692 | GPL570 |
|
MED, ID00277
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
ID00277
|
| Sample_geo_accession | GSM869692
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869692/suppl/GSM869692.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869693 | GPL570 |
|
MED, ID00288
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
ID00288
|
| Sample_geo_accession | GSM869693
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869693/suppl/GSM869693.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869694 | GPL570 |
|
MED, ID00330
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
ID00330
|
| Sample_geo_accession | GSM869694
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869694/suppl/GSM869694.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869695 | GPL570 |
|
MED, ID00437
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
ID00437
|
| Sample_geo_accession | GSM869695
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869695/suppl/GSM869695.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869696 | GPL570 |
|
MED, ID00565
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
ID00565
|
| Sample_geo_accession | GSM869696
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869696/suppl/GSM869696.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869700 | GPL570 |
|
MED, ID00797
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
ID00797
|
| Sample_geo_accession | GSM869700
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869700/suppl/GSM869700.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869707 | GPL570 |
|
NORMAL, PediatricCerebellum1
|
normal brain control, cerebellum, pediatric
|
tissue: normal cerebellum
developmental_stage: pediatric
|
Pediatric2
|
| Sample_geo_accession | GSM869707
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869707/suppl/GSM869707.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869708 | GPL570 |
|
NORMAL, PediatricFrontal1
|
normal brain control, frontal, pediatric
|
tissue: normal frontal
developmental_stage: pediatric
|
Pediatric3
|
| Sample_geo_accession | GSM869708
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869708/suppl/GSM869708.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869727 | GPL570 |
|
PNET, ID00079
|
brain tumor, primitive neuroectodermal tumor
|
tissue: primitive neuroectodermal tumor
|
ID00079
|
| Sample_geo_accession | GSM869727
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869727/suppl/GSM869727.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869728 | GPL570 |
|
PNET, ID00178
|
brain tumor, primitive neuroectodermal tumor
|
tissue: primitive neuroectodermal tumor
|
ID00178
|
| Sample_geo_accession | GSM869728
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869728/suppl/GSM869728.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869729 | GPL570 |
|
PNET, ID00224
|
brain tumor, primitive neuroectodermal tumor
|
tissue: primitive neuroectodermal tumor
|
ID00224
|
| Sample_geo_accession | GSM869729
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869729/suppl/GSM869729.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869730 | GPL570 |
|
PNET, ID00383
|
brain tumor, primitive neuroectodermal tumor
|
tissue: primitive neuroectodermal tumor
|
ID00383
|
| Sample_geo_accession | GSM869730
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869730/suppl/GSM869730.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869732 | GPL570 |
|
PNET, ID00536
|
brain tumor, primitive neuroectodermal tumor
|
tissue: primitive neuroectodermal tumor
|
ID00536
|
| Sample_geo_accession | GSM869732
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869732/suppl/GSM869732.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869733 | GPL570 |
|
PNET, ID00599
|
brain tumor, primitive neuroectodermal tumor
|
tissue: primitive neuroectodermal tumor
|
ID00599
|
| Sample_geo_accession | GSM869733
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869733/suppl/GSM869733.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869735 | GPL570 |
|
PNET, ID00760
|
brain tumor, primitive neuroectodermal tumor
|
tissue: primitive neuroectodermal tumor
|
ID00760
|
| Sample_geo_accession | GSM869735
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869735/suppl/GSM869735.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869736 | GPL570 |
|
PNET, ID00776
|
brain tumor, primitive neuroectodermal tumor
|
tissue: primitive neuroectodermal tumor
|
ID00776
|
| Sample_geo_accession | GSM869736
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869736/suppl/GSM869736.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM869737 | GPL570 |
|
PNET, ID00777
|
brain tumor, primitive neuroectodermal tumor
|
tissue: primitive neuroectodermal tumor
|
ID00777
|
| Sample_geo_accession | GSM869737
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Feb 01 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery.
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure.
| | Sample_scan_protocol | Standard Affymetrix procedure.
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM869nnn/GSM869737/suppl/GSM869737.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982838 | GPL570 |
|
ATRT, ID00818
|
brain tumor, atypical teratoid / rhabdoid tumor
|
tissue: atypical teratoid / rhabdoid tumor
|
brain tumor, atypical teratoid / rhabdoid tumor
|
| Sample_geo_accession | GSM982838
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982838/suppl/GSM982838_ATRT_ID00818_1_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982839 | GPL570 |
|
ATRT, ID00880
|
brain tumor, atypical teratoid / rhabdoid tumor
|
tissue: atypical teratoid / rhabdoid tumor
|
brain tumor, atypical teratoid / rhabdoid tumor
|
| Sample_geo_accession | GSM982839
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982839/suppl/GSM982839_ATRT_ID00880C_1_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982840 | GPL570 |
|
MED, ID00801
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
brain tumor, medulloblastoma
|
| Sample_geo_accession | GSM982840
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982840/suppl/GSM982840_LARGE_ID00801_1_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982841 | GPL570 |
|
MED_ID00851
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
brain tumor, medulloblastoma
|
| Sample_geo_accession | GSM982841
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982841/suppl/GSM982841_LARGE_ID00851_1_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982842 | GPL570 |
|
MED_ID00529
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
brain tumor, medulloblastoma
|
| Sample_geo_accession | GSM982842
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982842/suppl/GSM982842_MED_ID00529_1_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982843 | GPL570 |
|
MED_ID00719
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
brain tumor, medulloblastoma
|
| Sample_geo_accession | GSM982843
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982843/suppl/GSM982843_MED_ID00719_1_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982844 | GPL570 |
|
MED_ID00791
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
brain tumor, medulloblastoma
|
| Sample_geo_accession | GSM982844
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982844/suppl/GSM982844_MED_ID00791_1_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982845 | GPL570 |
|
MED_ID00877
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
brain tumor, medulloblastoma
|
| Sample_geo_accession | GSM982845
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982845/suppl/GSM982845_MED_ID00877_1_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982846 | GPL570 |
|
MED_ID00898
|
brain tumor, medulloblastoma
|
tissue: medulloblastoma
|
brain tumor, medulloblastoma
|
| Sample_geo_accession | GSM982846
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982846/suppl/GSM982846_MED_ID00898_1_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982847 | GPL570 |
|
NORMAL, PediatricOccipital1, ID00514
|
normal brain control, occipital, pediatric
|
tissue: normal brain
|
normal brain control, occipital, pediatric
|
| Sample_geo_accession | GSM982847
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982847/suppl/GSM982847_NORMAL_ID00514_Occipital_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982848 | GPL570 |
|
NORMAL, PediatricParietal1, ID00514
|
normal brain control, parietal, pediatric
|
tissue: normal brain
|
normal brain control, parietal, pediatric
|
| Sample_geo_accession | GSM982848
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982848/suppl/GSM982848_NORMAL_ID00514_Parietal_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982849 | GPL570 |
|
NORMAL, PediatricTemporal1, ID00514
|
normal brain control, temporal, pediatric
|
tissue: normal brain
|
normal brain control, temporal, pediatric
|
| Sample_geo_accession | GSM982849
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982849/suppl/GSM982849_NORMAL_ID00514_Temporal_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982850 | GPL570 |
|
NORMAL, PediatricCerebellum1, ID00605
|
normal brain control, cerebellum, pediatric
|
tissue: normal brain
|
normal brain control, cerebellum, pediatric
|
| Sample_geo_accession | GSM982850
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982850/suppl/GSM982850_NORMAL_ID00605_Cerebellum_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982851 | GPL570 |
|
NORMAL, PediatricOccipital2, ID00605
|
normal brain control, occipital, pediatric
|
tissue: normal brain
|
normal brain control, occipital, pediatric
|
| Sample_geo_accession | GSM982851
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982851/suppl/GSM982851_NORMAL_ID00605_Occipital_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982852 | GPL570 |
|
NORMAL, PediatricParietal2, ID00605
|
normal brain control, parietal, pediatric
|
tissue: normal brain
|
normal brain control, parietal, pediatric
|
| Sample_geo_accession | GSM982852
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982852/suppl/GSM982852_NORMAL_ID00605_Parietal_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
GSM982853 | GPL570 |
|
NORMAL, PediatricTemporal2, ID00605
|
normal brain control, temporal, pediatric
|
tissue: normal brain
|
normal brain control, temporal, pediatric
|
| Sample_geo_accession | GSM982853
| | Sample_status | Public on Jan 21 2013
| | Sample_submission_date | Aug 08 2012
| | Sample_last_update_date | Jan 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | n/a
| | Sample_growth_protocol_ch1 | All samples were collected at time of surgery
| | 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 most samples, 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 a few samples, limited amount of starting RNA precluded use of this protocol. Instead, 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 | Standard Affymetrix procedure
| | Sample_scan_protocol | Standard Affymetrix procedure
| | Sample_data_processing | Data were background corrected and normalized using gcRMA (as implemented in Bioconductor).
| | 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/GSM982nnn/GSM982853/suppl/GSM982853_NORMAL_ID00605_Temporal_AMBION.CEL.gz
| | Sample_series_id | GSE35493
| | Sample_data_row_count | 54674
| | |
|
| |
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