Search results for the GEO ID: GSE35426  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM868089 | GPL570 |
|
SMZL_GEP_C1unmut_7qdel
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL 7q deletion unmutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868089
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868089/suppl/GSM868089.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868090 | GPL570 |
|
SMZL_GEP_C2mut
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL mutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868090
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868090/suppl/GSM868090.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868091 | GPL570 |
|
SMZL_GEP_C3mut
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL mutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868091
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868091/suppl/GSM868091.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868092 | GPL570 |
|
SMZL_GEP_C4mut
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL mutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868092
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868092/suppl/GSM868092.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868093 | GPL570 |
|
SMZL_GEP_C5mut
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL mutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868093
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868093/suppl/GSM868093.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868094 | GPL570 |
|
SMZL_GEP_C6mut_7qdel
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL 7q deletion mutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868094
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868094/suppl/GSM868094.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868095 | GPL570 |
|
SMZL_GEP_C7unmut_7qdel
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL 7q deletion unmutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868095
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868095/suppl/GSM868095.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868096 | GPL570 |
|
SMZL_GEP_C8mut_7qdel
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL 7q deletion mutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868096
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868096/suppl/GSM868096.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868097 | GPL570 |
|
SMZL_GEP_C9mut_7qdel
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL 7q deletion mutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868097
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868097/suppl/GSM868097.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868098 | GPL570 |
|
SMZL_GEP_C10mut_7qdel
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL 7q deletion mutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868098
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868098/suppl/GSM868098.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868099 | GPL570 |
|
SMZL_GEP_C13mut
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL mutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868099
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868099/suppl/GSM868099.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868100 | GPL570 |
|
SMZL_GEP_8527mut
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL mutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868100
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868100/suppl/GSM868100.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868101 | GPL570 |
|
SMZL_GEP_8530unmut_7qdel
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL 7q deletion unmutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868101
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868101/suppl/GSM868101.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868102 | GPL570 |
|
SMZL_GEP_8536mut
|
Splenic marginal zone lymphoma with more than 70% tumour content
|
tumour: SMZL mutated
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868102
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868102/suppl/GSM868102.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868103 | GPL570 |
|
GEP_FL14
|
Follicular lymphoma from lymph node
|
tumour: FL
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868103
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868103/suppl/GSM868103.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868104 | GPL570 |
|
GEP_FL16
|
Follicular lymphoma from lymph node
|
tumour: FL
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868104
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868104/suppl/GSM868104.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868105 | GPL570 |
|
GEP_FL17
|
Follicular lymphoma from lymph node
|
tumour: FL
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868105
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868105/suppl/GSM868105.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868106 | GPL570 |
|
GEP_FL20
|
Follicular lymphoma from lymph node
|
tumour: FL
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868106
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868106/suppl/GSM868106.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868107 | GPL570 |
|
GEP_FL21
|
Follicular lymphoma from lymph node
|
tumour: FL
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868107
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868107/suppl/GSM868107.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868108 | GPL570 |
|
GEP_MCL22
|
Mantle cell lymphoma from lymph node
|
tumour: MCL
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868108
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868108/suppl/GSM868108.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868109 | GPL570 |
|
GEP_MCL23
|
Mantle cell lymphoma from lymph node
|
tumour: MCL
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868109
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868109/suppl/GSM868109.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868110 | GPL570 |
|
GEP_MCL24
|
Mantle cell lymphoma from lymph node
|
tumour: MCL
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868110
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868110/suppl/GSM868110.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
| | |
|
GSM868111 | GPL570 |
|
GEP_MCL25
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Mantle cell lymphoma from lymph node
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tumour: MCL
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Mutation is for IgH mutation and 7q deletion is tested by FISH
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| Sample_geo_accession | GSM868111
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868111/suppl/GSM868111.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
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GSM868112 | GPL570 |
|
GEP_MCL29
|
Mantle cell lymphoma from lymph node
|
tumour: MCL
|
Mutation is for IgH mutation and 7q deletion is tested by FISH
|
| Sample_geo_accession | GSM868112
| | Sample_status | Public on Aug 30 2012
| | Sample_submission_date | Jan 30 2012
| | Sample_last_update_date | Aug 30 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 | RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA
| | Sample_hyb_protocol | Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Batch GC-RMA Normalisation on all lymphomas samples ran on the HG-U133 plus2 GeneChips was carried out using the GC-RMA() function within the affy library version 2.8.4 in Bioconductor version 2.0. All GC-RMA data were logged. Bioconductor was run on R version 2.13.2 (2011-09-30). The file was written out and split into each individual sample file with one column for probe and another for the GC-RMA normalised value
| | Sample_platform_id | GPL570
| | Sample_contact_name | Alan,J,Watkins
| | Sample_contact_email | a.j.watkins@doctors.org.uk
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Addenbrooke's Hospital
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB2 0QQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM868nnn/GSM868112/suppl/GSM868112.CEL.gz
| | Sample_series_id | GSE21554
| | Sample_series_id | GSE35426
| | Sample_data_row_count | 54675
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