Search results for the GEO ID: GSE16155  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM404936 | GPL570 |
|
EPN_80, non-recurrent
|
EPN_80, non-recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404936
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404936/suppl/GSM404936.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404937 | GPL570 |
|
EPN_110, recurrent
|
EPN_110, recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404937
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404937/suppl/GSM404937.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404938 | GPL570 |
|
EPN_135, recurrent
|
EPN_135, recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404938
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404938/suppl/GSM404938.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404939 | GPL570 |
|
EPN_195, recurrent
|
EPN_195, recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404939
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404939/suppl/GSM404939.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404940 | GPL570 |
|
EPN_242, recurrent
|
EPN_242, recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404940
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404940/suppl/GSM404940.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404941 | GPL570 |
|
EPN_246, recurrent
|
EPN_246, recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404941
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404941/suppl/GSM404941.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404942 | GPL570 |
|
EPN_285, non-recurrent
|
EPN_285, non-recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404942
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404942/suppl/GSM404942.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404943 | GPL570 |
|
EPN_306, non-recurrent
|
EPN_306, non-recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404943
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404943/suppl/GSM404943.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404944 | GPL570 |
|
EPN_318, non-recurrent
|
EPN_318, non-recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404944
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404944/suppl/GSM404944.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404945 | GPL570 |
|
EPN_319, recurrent
|
EPN_319, recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404945
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404945/suppl/GSM404945.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404946 | GPL570 |
|
EPN_364, recurrent
|
EPN_364, recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404946
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404946/suppl/GSM404946.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404947 | GPL570 |
|
EPN_388, non-recurrent
|
EPN_388, non-recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404947
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404947/suppl/GSM404947.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404948 | GPL570 |
|
EPN_392, non-recurrent
|
EPN_392, non-recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404948
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404948/suppl/GSM404948.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404949 | GPL570 |
|
EPN_393, recurrent
|
EPN_393, recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404949
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404949/suppl/GSM404949.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404950 | GPL570 |
|
EPN_416, non-recurrent
|
EPN_416, non-recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404950
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404950/suppl/GSM404950.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404951 | GPL570 |
|
EPN_419, non-recurrent
|
EPN_419, non-recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404951
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404951/suppl/GSM404951.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404952 | GPL570 |
|
EPN_459, non-recurrent
|
EPN_459, non-recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404952
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404952/suppl/GSM404952.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404953 | GPL570 |
|
EPN_483, recurrent
|
EPN_483, recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404953
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404953/suppl/GSM404953.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
GSM404954 | GPL570 |
|
EPN_507, recurrent
|
EPN_507, recurrent
|
tissue: brain tumor (ependymoma)
genotype: brain tumor (ependymoma)
|
Gene expression data from surgical tumor sample of ependymoma
|
| Sample_geo_accession | GSM404954
| | Sample_status | Public on Oct 01 2009
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Feb 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
| | Sample_extract_protocol_ch1 | RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
| | Sample_data_processing | Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andrew,M,Donson
| | Sample_contact_email | andrew.donson@ucdenver.edu
| | Sample_contact_phone | 303 724 4012
| | Sample_contact_fax | 303 724 4015
| | Sample_contact_laboratory | RC1 North, P18-4401M
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | UC Denver
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80010
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404954/suppl/GSM404954.CEL.gz
| | Sample_series_id | GSE16155
| | Sample_data_row_count | 18624
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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