Search results for the GEO ID: GSE39339  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM966228 | GPL570 |
|
Day 0, Patient 184 with good risk
|
BCR-ABL patient with good risk before treatment (day 0)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: good
treatment: none
time point: day 0
patient identifier: 184
|
GR_184_Day 0
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966228
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966228/suppl/GSM966228_GR_184_D0.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966229 | GPL570 |
|
Day 0, Patient 193 with good risk
|
BCR-ABL patient with good risk before treatment (day 0)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: good
treatment: none
time point: day 0
patient identifier: 193
|
GR_193_Day 0
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966229
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966229/suppl/GSM966229_GR_193_D0.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966230 | GPL570 |
|
Day 0, Patient 277 with good risk
|
BCR-ABL patient with good risk before treatment (day 0)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: good
treatment: none
time point: day 0
patient identifier: 277
|
GR_277_Day 0
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966230
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966230/suppl/GSM966230_GR_277_D0.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966231 | GPL570 |
|
Day 0, Patient 341 with good risk
|
BCR-ABL patient with good risk before treatment (day 0)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: good
treatment: none
time point: day 0
patient identifier: 341
|
GR_341_Day 0
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966231
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966231/suppl/GSM966231_GR_341_D0.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966232 | GPL570 |
|
Day 17, Patient 184 with good risk
|
BCR-ABL patient with good risk after treatment (day 17)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: good
treatment: dexamethasone, anthracycline, vincristine, L-Asparaginase
time point: day 17
patient identifier: 184
|
GR_184_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966232
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966232/suppl/GSM966232_GR_184_D17.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966233 | GPL570 |
|
Day 17, Patient 256 with good risk
|
BCR-ABL patient with good risk after treatment (day 17)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: good
treatment: dexamethasone, anthracycline, vincristine, L-Asparaginase
time point: day 17
patient identifier: 256
|
GR_256_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966233
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966233/suppl/GSM966233_GR_256_D17.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966234 | GPL570 |
|
Day 17, Patient 277 with good risk
|
BCR-ABL patient with good risk after treatment (day 17)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: good
treatment: dexamethasone, anthracycline, vincristine, L-Asparaginase
time point: day 17
patient identifier: 277
|
GR_277_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966234
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966234/suppl/GSM966234_GR_277_D17.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966235 | GPL570 |
|
Day 17, Patient 319 with good risk
|
BCR-ABL patient with good risk after treatment (day 17)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: good
treatment: dexamethasone, anthracycline, vincristine, L-Asparaginase
time point: day 17
patient identifier: 319
|
GR_319_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966235
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966235/suppl/GSM966235_GR_319_D17.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966236 | GPL570 |
|
Day 0, Patient 205 with poor risk
|
BCR-ABL patient with poor risk before treatment (day 0)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: poor
treatment: none
time point: day 0
patient identifier: 205
|
PR_205_Day 0
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966236
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966236/suppl/GSM966236_PR_205_D0.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966237 | GPL570 |
|
Day 0, Patient 241 with poor risk
|
BCR-ABL patient with poor risk before treatment (day 0)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: poor
treatment: none
time point: day 0
patient identifier: 241
|
PR_241_Day 0
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966237
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966237/suppl/GSM966237_PR_241_D0.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966238 | GPL570 |
|
Day 17, Patient 205 with poor risk
|
BCR-ABL patient with poor risk after treatment (day 17)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: poor
treatment: dexamethasone, anthracycline, vincristine, L-Asparaginase
time point: day 17
patient identifier: 205
|
PR_205_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966238
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966238/suppl/GSM966238_PR_205_D17.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966239 | GPL570 |
|
Day 17, Patient 205 (replicate) with poor risk
|
BCR-ABL patient with poor risk after treatment (day 17)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: poor
treatment: dexamethasone, anthracycline, vincristine, L-Asparaginase
time point: day 17
patient identifier: 205
|
PR_205_rep_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966239
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966239/suppl/GSM966239_PR_205_D17_REP.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966240 | GPL570 |
|
Day 17, Patient 320 with poor risk
|
BCR-ABL patient with poor risk after treatment (day 17)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: poor
treatment: dexamethasone, anthracycline, vincristine, L-Asparaginase
time point: day 17
patient identifier: 320
|
PR_320_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966240
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966240/suppl/GSM966240_PR_320_D17.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966241 | GPL570 |
|
Day 17, Patient 345with poor risk
|
BCR-ABL patient with poor risk after treatment (day 17)
|
tissue: bone marrow cells
developmental stage: child
disease state: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)
risk: poor
treatment: dexamethasone, anthracycline, vincristine, L-Asparaginase
time point: day 17
patient identifier: 345
|
PR_345_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).
|
| Sample_geo_accession | GSM966241
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.
| | Sample_growth_protocol_ch1 | Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966241/suppl/GSM966241_PR_345_D17.CEL.gz
| | Sample_series_id | GSE39335
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966244 | GPL570 |
|
0 h, CCRF-CEM-C7-14, biological rep1
|
CCRF-CEM-C7-14 before dexamethasone treatment (0 h)
|
cell line: CCRF-CEM-C7-14
cell type: leukemia
treatment: none
time point: 0 h
|
T0-1
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL
|
| Sample_geo_accession | GSM966244
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 1 µM dexamethasone (Dex) (Sigma, MO, USA) at the indicated time points (0, 2 and 10 h).
| | Sample_growth_protocol_ch1 | CCRF-CEM-C7-14 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin (Cambrex, NJ, USA) and were seeded into 60 mm plates for RNA extraction. Prior to the hormone treatment, the media was changed to RPMI-1640 supplemented with 10% charcoal-stripped fetal bovine serum (HyClone, UT, USA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested and the total RNA was extracted using the RNeasy® Plus Mini Kit and QIAshredder (Qiagen, Hilden, Germany), following the manufacturer's guidelines. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies), and RNA quality was determined by means of an RNA 6000 NanoAssay on an Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966244/suppl/GSM966244_T0-1.CEL.gz
| | Sample_series_id | GSE39338
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966245 | GPL570 |
|
0 h, CCRF-CEM-C7-14, biological rep2
|
CCRF-CEM-C7-14 before dexamethasone treatment (0 h)
|
cell line: CCRF-CEM-C7-14
cell type: leukemia
treatment: none
time point: 0 h
|
T0-2
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL
|
| Sample_geo_accession | GSM966245
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 1 µM dexamethasone (Dex) (Sigma, MO, USA) at the indicated time points (0, 2 and 10 h).
| | Sample_growth_protocol_ch1 | CCRF-CEM-C7-14 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin (Cambrex, NJ, USA) and were seeded into 60 mm plates for RNA extraction. Prior to the hormone treatment, the media was changed to RPMI-1640 supplemented with 10% charcoal-stripped fetal bovine serum (HyClone, UT, USA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested and the total RNA was extracted using the RNeasy® Plus Mini Kit and QIAshredder (Qiagen, Hilden, Germany), following the manufacturer's guidelines. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies), and RNA quality was determined by means of an RNA 6000 NanoAssay on an Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966245/suppl/GSM966245_T0-2.CEL.gz
| | Sample_series_id | GSE39338
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966246 | GPL570 |
|
0 h, CCRF-CEM-C7-14, biological rep3
|
CCRF-CEM-C7-14 before dexamethasone treatment (0 h)
|
cell line: CCRF-CEM-C7-14
cell type: leukemia
treatment: none
time point: 0 h
|
T0-3
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL
|
| Sample_geo_accession | GSM966246
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 1 µM dexamethasone (Dex) (Sigma, MO, USA) at the indicated time points (0, 2 and 10 h).
| | Sample_growth_protocol_ch1 | CCRF-CEM-C7-14 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin (Cambrex, NJ, USA) and were seeded into 60 mm plates for RNA extraction. Prior to the hormone treatment, the media was changed to RPMI-1640 supplemented with 10% charcoal-stripped fetal bovine serum (HyClone, UT, USA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested and the total RNA was extracted using the RNeasy® Plus Mini Kit and QIAshredder (Qiagen, Hilden, Germany), following the manufacturer's guidelines. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies), and RNA quality was determined by means of an RNA 6000 NanoAssay on an Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966246/suppl/GSM966246_T0-3.CEL.gz
| | Sample_series_id | GSE39338
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966247 | GPL570 |
|
2 h, CCRF-CEM-C7-14, biological rep1
|
CCRF-CEM-C7-14 with dexamethasone treatment for 2 h
|
cell line: CCRF-CEM-C7-14
cell type: leukemia
treatment: dexamethasone
time point: 2 h
|
T2-1
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL
|
| Sample_geo_accession | GSM966247
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 1 µM dexamethasone (Dex) (Sigma, MO, USA) at the indicated time points (0, 2 and 10 h).
| | Sample_growth_protocol_ch1 | CCRF-CEM-C7-14 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin (Cambrex, NJ, USA) and were seeded into 60 mm plates for RNA extraction. Prior to the hormone treatment, the media was changed to RPMI-1640 supplemented with 10% charcoal-stripped fetal bovine serum (HyClone, UT, USA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested and the total RNA was extracted using the RNeasy® Plus Mini Kit and QIAshredder (Qiagen, Hilden, Germany), following the manufacturer's guidelines. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies), and RNA quality was determined by means of an RNA 6000 NanoAssay on an Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966247/suppl/GSM966247_T2-1.CEL.gz
| | Sample_series_id | GSE39338
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966248 | GPL570 |
|
2 h, CCRF-CEM-C7-14, biological rep2
|
CCRF-CEM-C7-14 with dexamethasone treatment for 2 h
|
cell line: CCRF-CEM-C7-14
cell type: leukemia
treatment: dexamethasone
time point: 2 h
|
T2-2
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL
|
| Sample_geo_accession | GSM966248
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 1 µM dexamethasone (Dex) (Sigma, MO, USA) at the indicated time points (0, 2 and 10 h).
| | Sample_growth_protocol_ch1 | CCRF-CEM-C7-14 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin (Cambrex, NJ, USA) and were seeded into 60 mm plates for RNA extraction. Prior to the hormone treatment, the media was changed to RPMI-1640 supplemented with 10% charcoal-stripped fetal bovine serum (HyClone, UT, USA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested and the total RNA was extracted using the RNeasy® Plus Mini Kit and QIAshredder (Qiagen, Hilden, Germany), following the manufacturer's guidelines. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies), and RNA quality was determined by means of an RNA 6000 NanoAssay on an Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966248/suppl/GSM966248_T2-2.CEL.gz
| | Sample_series_id | GSE39338
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966249 | GPL570 |
|
2 h, CCRF-CEM-C7-14, biological rep3
|
CCRF-CEM-C7-14 with dexamethasone treatment for 2 h
|
cell line: CCRF-CEM-C7-14
cell type: leukemia
treatment: dexamethasone
time point: 2 h
|
T2-3
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL
|
| Sample_geo_accession | GSM966249
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 1 µM dexamethasone (Dex) (Sigma, MO, USA) at the indicated time points (0, 2 and 10 h).
| | Sample_growth_protocol_ch1 | CCRF-CEM-C7-14 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin (Cambrex, NJ, USA) and were seeded into 60 mm plates for RNA extraction. Prior to the hormone treatment, the media was changed to RPMI-1640 supplemented with 10% charcoal-stripped fetal bovine serum (HyClone, UT, USA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested and the total RNA was extracted using the RNeasy® Plus Mini Kit and QIAshredder (Qiagen, Hilden, Germany), following the manufacturer's guidelines. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies), and RNA quality was determined by means of an RNA 6000 NanoAssay on an Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966249/suppl/GSM966249_T2-3.CEL.gz
| | Sample_series_id | GSE39338
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966250 | GPL570 |
|
10 h, CCRF-CEM-C7-14, biological rep1
|
CCRF-CEM-C7-14 with dexamethasone treatment for 10 h
|
cell line: CCRF-CEM-C7-14
cell type: leukemia
treatment: dexamethasone
time point: 10 h
|
T10-1
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL
|
| Sample_geo_accession | GSM966250
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 1 µM dexamethasone (Dex) (Sigma, MO, USA) at the indicated time points (0, 2 and 10 h).
| | Sample_growth_protocol_ch1 | CCRF-CEM-C7-14 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin (Cambrex, NJ, USA) and were seeded into 60 mm plates for RNA extraction. Prior to the hormone treatment, the media was changed to RPMI-1640 supplemented with 10% charcoal-stripped fetal bovine serum (HyClone, UT, USA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested and the total RNA was extracted using the RNeasy® Plus Mini Kit and QIAshredder (Qiagen, Hilden, Germany), following the manufacturer's guidelines. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies), and RNA quality was determined by means of an RNA 6000 NanoAssay on an Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966250/suppl/GSM966250_T10-1.CEL.gz
| | Sample_series_id | GSE39338
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
|
GSM966251 | GPL570 |
|
10 h, CCRF-CEM-C7-14, biological rep2
|
CCRF-CEM-C7-14 with dexamethasone treatment for 10 h
|
cell line: CCRF-CEM-C7-14
cell type: leukemia
treatment: dexamethasone
time point: 10 h
|
T10-2
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL
|
| Sample_geo_accession | GSM966251
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Jul 13 2012
| | Sample_last_update_date | Jul 30 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 1 µM dexamethasone (Dex) (Sigma, MO, USA) at the indicated time points (0, 2 and 10 h).
| | Sample_growth_protocol_ch1 | CCRF-CEM-C7-14 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin (Cambrex, NJ, USA) and were seeded into 60 mm plates for RNA extraction. Prior to the hormone treatment, the media was changed to RPMI-1640 supplemented with 10% charcoal-stripped fetal bovine serum (HyClone, UT, USA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested and the total RNA was extracted using the RNeasy® Plus Mini Kit and QIAshredder (Qiagen, Hilden, Germany), following the manufacturer's guidelines. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies), and RNA quality was determined by means of an RNA 6000 NanoAssay on an Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix protocol.
| | Sample_hyb_protocol | Standard Affymetrix protocol.
| | Sample_scan_protocol | Affymetric GeneChip Scanner 3000 7G
| | Sample_data_processing | Probes were normalized using the RMA normalization method (R with Bioconductor).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Daphne,,Chen
| | Sample_contact_email | Daphnewei-chen.Chen@postgrad.manchester.ac.uk
| | Sample_contact_institute | University of Manchester
| | Sample_contact_address | Oxford Road
| | Sample_contact_city | Manchester
| | Sample_contact_zip/postal_code | M13 9PT
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM966nnn/GSM966251/suppl/GSM966251_T10-2.CEL.gz
| | Sample_series_id | GSE39338
| | Sample_series_id | GSE39339
| | Sample_data_row_count | 54675
| | |
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