Search results for the GEO ID: GSE44971  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1094814 | GPL570 |
|
PA_62
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 21
gender: Male
dna methylation subgroup: NA
mapk hit: Pilocytic astrocytoma: None identified
|
|
| Sample_geo_accession | GSM1094814
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094814/suppl/GSM1094814_DKFZ0686.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094815 | GPL570 |
|
PA_01
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 9
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094815
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094815/suppl/GSM1094815_DKFZ0692.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094816 | GPL570 |
|
PA_63
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebral hemisphere
age at diagnosis (years): 17
gender: Male
dna methylation subgroup: NA
mapk hit: Pilocytic astrocytoma: None identified
|
|
| Sample_geo_accession | GSM1094816
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094816/suppl/GSM1094816_DKFZ0693.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094817 | GPL570 |
|
PA_02
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 4
gender: Female
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094817
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094817/suppl/GSM1094817_DKFZ0694.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094818 | GPL570 |
|
PA_03
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 5
gender: Female
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094818
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094818/suppl/GSM1094818_DKFZ0687.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094819 | GPL570 |
|
PA_04
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebral hemisphere
age at diagnosis (years): 16
gender: Male
dna methylation subgroup: 1
mapk hit: Pilocytic astrocytoma: FAM131B:BRAF fusion
|
|
| Sample_geo_accession | GSM1094819
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094819/suppl/GSM1094819_DKFZ0695.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094820 | GPL570 |
|
PA_05
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 2
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9
|
|
| Sample_geo_accession | GSM1094820
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094820/suppl/GSM1094820_DKFZ0696.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094821 | GPL570 |
|
PA_06
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 11
gender: Female
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9
|
|
| Sample_geo_accession | GSM1094821
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094821/suppl/GSM1094821_DKFZ0697.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094822 | GPL570 |
|
PA_08
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 4
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094822
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094822/suppl/GSM1094822_DKFZ0688.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094823 | GPL570 |
|
PA_09
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 16
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094823
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094823/suppl/GSM1094823_DKFZ0698.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094824 | GPL570 |
|
PA_10
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebral hemisphere
age at diagnosis (years): 14
gender: Male
dna methylation subgroup: 1
mapk hit: Pilocytic astrocytoma: BRAF V600E
|
|
| Sample_geo_accession | GSM1094824
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094824/suppl/GSM1094824_DKFZ0699.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094825 | GPL570 |
|
PA_11
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Diencephalon
age at diagnosis (years): 2
gender: Female
dna methylation subgroup: 1
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_breakpoint not determined
|
|
| Sample_geo_accession | GSM1094825
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094825/suppl/GSM1094825_DKFZ0700.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094826 | GPL570 |
|
PA_12
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 10
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9
|
|
| Sample_geo_accession | GSM1094826
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094826/suppl/GSM1094826_DKFZ0689.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094827 | GPL570 |
|
PA_13
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 13
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094827
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094827/suppl/GSM1094827_DKFZ0701.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094828 | GPL570 |
|
PA_15
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Diencephalon
age at diagnosis (years): 3
gender: Male
dna methylation subgroup: 1
mapk hit: Pilocytic astrocytoma: NF1; KIAA1549:BRAF fusion_breakpoint not determined
|
|
| Sample_geo_accession | GSM1094828
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094828/suppl/GSM1094828_DKFZ0702.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094829 | GPL570 |
|
PA_16
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 19
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9
|
|
| Sample_geo_accession | GSM1094829
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094829/suppl/GSM1094829_DKFZ0703.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094830 | GPL570 |
|
PA_17
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 11
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:11
|
|
| Sample_geo_accession | GSM1094830
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094830/suppl/GSM1094830_DKFZ0704.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094831 | GPL570 |
|
PA_18
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Diencephalon
age at diagnosis (years): 3
gender: Female
dna methylation subgroup: 1
mapk hit: Pilocytic astrocytoma: NF1; KIAA1549:BRAF fusion_15:9; BRAF V600E
|
|
| Sample_geo_accession | GSM1094831
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094831/suppl/GSM1094831_DKFZ0705.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094832 | GPL570 |
|
PA_19
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 17
gender: Female
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: BRAF ins598T
|
|
| Sample_geo_accession | GSM1094832
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094832/suppl/GSM1094832_DKFZ0706.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094833 | GPL570 |
|
PA_20
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Diencephalon
age at diagnosis (years): 12
gender: Female
dna methylation subgroup: 1
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094833
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094833/suppl/GSM1094833_DKFZ0707.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094834 | GPL570 |
|
PA_22
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 22
gender: Female
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094834
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094834/suppl/GSM1094834_DKFZ0708.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094835 | GPL570 |
|
PA_23
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 11
gender: Female
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KRAS E63K
|
|
| Sample_geo_accession | GSM1094835
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094835/suppl/GSM1094835_DKFZ0709.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094836 | GPL570 |
|
PA_24
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 10
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094836
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094836/suppl/GSM1094836_DKFZ0710.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094837 | GPL570 |
|
PA_25
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Diencephalon
age at diagnosis (years): 3
gender: Female
dna methylation subgroup: 1
mapk hit: Pilocytic astrocytoma: BRAF V600E
|
|
| Sample_geo_accession | GSM1094837
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094837/suppl/GSM1094837_DKFZ0711.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094838 | GPL570 |
|
PA_26
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 2
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094838
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094838/suppl/GSM1094838_DKFZ0712.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094839 | GPL570 |
|
PA_27
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 4
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094839
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094839/suppl/GSM1094839_DKFZ0713.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094841 | GPL570 |
|
PA_29
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 5
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094841
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094841/suppl/GSM1094841_DKFZ0715.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094842 | GPL570 |
|
PA_31
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Brainstem
age at diagnosis (years): 7
gender: Male
dna methylation subgroup: 1
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9
|
|
| Sample_geo_accession | GSM1094842
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094842/suppl/GSM1094842_DKFZ0716.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094843 | GPL570 |
|
PA_32
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebral hemisphere
age at diagnosis (years): 8
gender: Female
dna methylation subgroup: 1
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9
|
|
| Sample_geo_accession | GSM1094843
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094843/suppl/GSM1094843_DKFZ0717.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094844 | GPL570 |
|
PA_36
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 4
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094844
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094844/suppl/GSM1094844_DKFZ0690.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094845 | GPL570 |
|
PA_37
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 6
gender: Female
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094845
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094845/suppl/GSM1094845_DKFZ0691.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094846 | GPL570 |
|
PA_64
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 20
gender: Female
dna methylation subgroup: NA
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094846
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094846/suppl/GSM1094846_DKFZ0718.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094847 | GPL570 |
|
PA_40
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 14
gender: Female
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: None identified
|
|
| Sample_geo_accession | GSM1094847
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094847/suppl/GSM1094847_DKFZ0281.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094848 | GPL570 |
|
PA_44
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Fourth Ventricle
age at diagnosis (years): 9
gender: Male
dna methylation subgroup: 1
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094848
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094848/suppl/GSM1094848_DKFZ0282.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094849 | GPL570 |
|
PA_65
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 25
gender: Male
dna methylation subgroup: NA
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:11
|
|
| Sample_geo_accession | GSM1094849
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094849/suppl/GSM1094849_DKFZ0719.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094850 | GPL570 |
|
PA_66
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 26
gender: Female
dna methylation subgroup: NA
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094850
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094850/suppl/GSM1094850_DKFZ0720.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094851 | GPL570 |
|
PA_47
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 4
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094851
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094851/suppl/GSM1094851_DKFZ0284.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094852 | GPL570 |
|
PA_67
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 20
gender: Female
dna methylation subgroup: NA
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094852
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094852/suppl/GSM1094852_DKFZ0721.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094853 | GPL570 |
|
PA_68
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 16
gender: Male
dna methylation subgroup: NA
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094853
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094853/suppl/GSM1094853_DKFZ0286.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094854 | GPL570 |
|
PA_69
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Left frontal lobe
age at diagnosis (years): 12
gender: Female
dna methylation subgroup: NA
mapk hit: Pilocytic astrocytoma: NF1
|
|
| Sample_geo_accession | GSM1094854
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094854/suppl/GSM1094854_DKFZ0722.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094855 | GPL570 |
|
PA_54
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 3
gender: Female
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094855
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094855/suppl/GSM1094855_DKFZ0277.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094856 | GPL570 |
|
PA_56
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 11
gender: Female
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094856
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094856/suppl/GSM1094856_DKFZ0667.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094857 | GPL570 |
|
PA_57
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 9
gender: Female
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094857
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094857/suppl/GSM1094857_DKFZ0290.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094858 | GPL570 |
|
PA_70
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 26
gender: Female
dna methylation subgroup: NA
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_15:9
|
|
| Sample_geo_accession | GSM1094858
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094858/suppl/GSM1094858_DKFZ0723.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094859 | GPL570 |
|
PA_58
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 3
gender: Male
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094859
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094859/suppl/GSM1094859_DKFZ0291.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094860 | GPL570 |
|
PA_59
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Optic nerve
age at diagnosis (years): 3
gender: Female
dna methylation subgroup: 1
mapk hit: Pilocytic astrocytoma: BRAF V600E
|
|
| Sample_geo_accession | GSM1094860
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094860/suppl/GSM1094860_DKFZ0278.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094861 | GPL570 |
|
PA_60
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Cerebellum
age at diagnosis (years): 8
gender: Female
dna methylation subgroup: 2
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094861
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094861/suppl/GSM1094861_DKFZ0279.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094862 | GPL570 |
|
PA_61
|
Frozen pilocytic astrocytoma tumor tissue
|
tissue: Pilocytic astrocytoma
brain location: Diencephalon
age at diagnosis (years): 12
gender: Male
dna methylation subgroup: 1
mapk hit: Pilocytic astrocytoma: KIAA1549:BRAF fusion_16:9
|
|
| Sample_geo_accession | GSM1094862
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094862/suppl/GSM1094862_DKFZ0280.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094863 | GPL570 |
|
CTRL_CBM_07
|
Normal cerebellum RNA (commercial source)
|
tissue: Normal cerebellum control
brain location: Cerebellum
age at diagnosis (years): Fetal
gender: Female
dna methylation subgroup: N/A
mapk hit: Pilocytic astrocytoma: N/A
|
|
| Sample_geo_accession | GSM1094863
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094863/suppl/GSM1094863_DKFZ0888.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094864 | GPL570 |
|
CTRL_CBM_08
|
Normal cerebellum RNA (commercial source)
|
tissue: Normal cerebellum control
brain location: Cerebellum
age at diagnosis (years): Fetal
gender: Female
dna methylation subgroup: N/A
mapk hit: Pilocytic astrocytoma: N/A
|
|
| Sample_geo_accession | GSM1094864
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094864/suppl/GSM1094864_DKFZ0889.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094866 | GPL570 |
|
CTRL_CBM_10
|
Normal cerebellum RNA (commercial source)
|
tissue: Normal cerebellum control
brain location: Cerebellum
age at diagnosis (years): Fetal
gender: Male
dna methylation subgroup: N/A
mapk hit: Pilocytic astrocytoma: N/A
|
|
| Sample_geo_accession | GSM1094866
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094866/suppl/GSM1094866_DKFZ0891.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094867 | GPL570 |
|
CTRL_CBM_11
|
Normal cerebellum RNA (commercial source)
|
tissue: Normal cerebellum control
brain location: Cerebellum
age at diagnosis (years): Fetal
gender: Female
dna methylation subgroup: N/A
mapk hit: Pilocytic astrocytoma: N/A
|
|
| Sample_geo_accession | GSM1094867
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094867/suppl/GSM1094867_DKFZ0892.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094868 | GPL570 |
|
CTRL_CBM_12
|
Normal cerebellum RNA (commercial source)
|
tissue: Normal cerebellum control
brain location: Cerebellum
age at diagnosis (years): 24
gender: Male
dna methylation subgroup: N/A
mapk hit: Pilocytic astrocytoma: N/A
|
|
| Sample_geo_accession | GSM1094868
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094868/suppl/GSM1094868_DKFZ0894.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094869 | GPL570 |
|
CTRL_CBM_13
|
Normal cerebellum RNA (commercial source)
|
tissue: Normal cerebellum control
brain location: Cerebellum
age at diagnosis (years): Adult
gender: Male
dna methylation subgroup: N/A
mapk hit: Pilocytic astrocytoma: N/A
|
|
| Sample_geo_accession | GSM1094869
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094869/suppl/GSM1094869_DKFZ0895.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094870 | GPL570 |
|
CTRL_CBM_14
|
Normal cerebellum RNA (commercial source)
|
tissue: Normal cerebellum control
brain location: Cerebellum
age at diagnosis (years): Adult
gender: Male
dna methylation subgroup: N/A
mapk hit: Pilocytic astrocytoma: N/A
|
|
| Sample_geo_accession | GSM1094870
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094870/suppl/GSM1094870_DKFZ0896.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
|
GSM1094871 | GPL570 |
|
CTRL_CBM_15
|
Normal cerebellum RNA (commercial source)
|
tissue: Normal cerebellum control
brain location: Cerebellum
age at diagnosis (years): 26
gender: Male
dna methylation subgroup: N/A
mapk hit: Pilocytic astrocytoma: N/A
|
|
| Sample_geo_accession | GSM1094871
| | Sample_status | Public on Jun 12 2013
| | Sample_submission_date | Mar 08 2013
| | Sample_last_update_date | Jun 12 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing = For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 | 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Marcel,,Kool
| | Sample_contact_email | m.kool@dkfz.de
| | Sample_contact_phone | 00496221424636
| | Sample_contact_department | Pediatric Neuro Oncology
| | Sample_contact_institute | German Cancer Research Center
| | Sample_contact_address | Im Neuenheimer Feld 580
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1094nnn/GSM1094871/suppl/GSM1094871_DKFZ0897.CEL.gz
| | Sample_series_id | GSE44971
| | Sample_data_row_count | 54675
| | |
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(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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