Search results for the GEO ID: GSE28327  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM700581 | GPL570 |
|
Myeloma tumor, sample 1
|
Bone marrow, tumor cells, MM
|
tissue: bone marrow
cell type: CD138+ tumor plasma cells
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_TUMOR_01
Newly diagnosed patient.
|
| Sample_geo_accession | GSM700581
| | Sample_status | Public on Apr 02 2011
| | Sample_submission_date | Apr 01 2011
| | Sample_last_update_date | Apr 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were untreated.
| | Sample_growth_protocol_ch1 | For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).
| | Sample_hyb_protocol | RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Chips were scanned on a GeneArray scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Olcay,,Batuman
| | Sample_contact_institute | SUNY Downstate Medical Center
| | Sample_contact_address | 450 Clarkson Ave, Box 20
| | Sample_contact_city | Brooklyn
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 11203
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM700nnn/GSM700581/suppl/GSM700581.CEL.gz
| | Sample_series_id | GSE28327
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700582 | GPL570 |
|
Myeloma tumor, sample 2
|
Bone marrow, tumor cells, MM
|
tissue: bone marrow
cell type: CD138+ tumor plasma cells
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_TUMOR_02
Newly diagnosed patient.
|
| Sample_geo_accession | GSM700582
| | Sample_status | Public on Apr 02 2011
| | Sample_submission_date | Apr 01 2011
| | Sample_last_update_date | Apr 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were untreated.
| | Sample_growth_protocol_ch1 | For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).
| | Sample_hyb_protocol | RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Chips were scanned on a GeneArray scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Olcay,,Batuman
| | Sample_contact_institute | SUNY Downstate Medical Center
| | Sample_contact_address | 450 Clarkson Ave, Box 20
| | Sample_contact_city | Brooklyn
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 11203
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM700nnn/GSM700582/suppl/GSM700582.CEL.gz
| | Sample_series_id | GSE28327
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700583 | GPL570 |
|
Myeloma tumor, sample 3
|
Bone marrow, tumor cells, MM
|
tissue: bone marrow
cell type: CD138+ tumor plasma cells
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_TUMOR_03
Newly diagnosed patient.
|
| Sample_geo_accession | GSM700583
| | Sample_status | Public on Apr 02 2011
| | Sample_submission_date | Apr 01 2011
| | Sample_last_update_date | Apr 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were untreated.
| | Sample_growth_protocol_ch1 | For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).
| | Sample_hyb_protocol | RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Chips were scanned on a GeneArray scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Olcay,,Batuman
| | Sample_contact_institute | SUNY Downstate Medical Center
| | Sample_contact_address | 450 Clarkson Ave, Box 20
| | Sample_contact_city | Brooklyn
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 11203
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM700nnn/GSM700583/suppl/GSM700583.CEL.gz
| | Sample_series_id | GSE28327
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700584 | GPL570 |
|
Myeloma tumor, sample 4
|
Bone marrow, tumor cells, MM
|
tissue: bone marrow
cell type: CD138+ tumor plasma cells
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_TUMOR_04
Newly diagnosed patient.
|
| Sample_geo_accession | GSM700584
| | Sample_status | Public on Apr 02 2011
| | Sample_submission_date | Apr 01 2011
| | Sample_last_update_date | Apr 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were untreated.
| | Sample_growth_protocol_ch1 | For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).
| | Sample_hyb_protocol | RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Chips were scanned on a GeneArray scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Olcay,,Batuman
| | Sample_contact_institute | SUNY Downstate Medical Center
| | Sample_contact_address | 450 Clarkson Ave, Box 20
| | Sample_contact_city | Brooklyn
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 11203
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM700nnn/GSM700584/suppl/GSM700584.CEL.gz
| | Sample_series_id | GSE28327
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700585 | GPL570 |
|
Myeloma tumor, sample 5
|
Bone marrow, tumor cells, MM
|
tissue: bone marrow
cell type: CD138+ tumor plasma cells
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_TUMOR_05
Newly diagnosed patient.
|
| Sample_geo_accession | GSM700585
| | Sample_status | Public on Apr 02 2011
| | Sample_submission_date | Apr 01 2011
| | Sample_last_update_date | Apr 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were untreated.
| | Sample_growth_protocol_ch1 | For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).
| | Sample_hyb_protocol | RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Chips were scanned on a GeneArray scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Olcay,,Batuman
| | Sample_contact_institute | SUNY Downstate Medical Center
| | Sample_contact_address | 450 Clarkson Ave, Box 20
| | Sample_contact_city | Brooklyn
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 11203
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM700nnn/GSM700585/suppl/GSM700585.CEL.gz
| | Sample_series_id | GSE28327
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700586 | GPL570 |
|
Myeloma tumor, sample 6
|
Bone marrow, tumor cells, MM
|
tissue: bone marrow
cell type: CD138+ tumor plasma cells
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_TUMOR_06
Newly diagnosed patient.
|
| Sample_geo_accession | GSM700586
| | Sample_status | Public on Apr 02 2011
| | Sample_submission_date | Apr 01 2011
| | Sample_last_update_date | Apr 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were untreated.
| | Sample_growth_protocol_ch1 | For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).
| | Sample_hyb_protocol | RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Chips were scanned on a GeneArray scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Olcay,,Batuman
| | Sample_contact_institute | SUNY Downstate Medical Center
| | Sample_contact_address | 450 Clarkson Ave, Box 20
| | Sample_contact_city | Brooklyn
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 11203
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM700nnn/GSM700586/suppl/GSM700586.CEL.gz
| | Sample_series_id | GSE28327
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700587 | GPL570 |
|
Myeloma tumor, sample 7
|
Bone marrow, tumor cells, MM
|
tissue: bone marrow
cell type: CD138+ tumor plasma cells
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_TUMOR_07
Newly diagnosed patient.
|
| Sample_geo_accession | GSM700587
| | Sample_status | Public on Apr 02 2011
| | Sample_submission_date | Apr 01 2011
| | Sample_last_update_date | Apr 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were untreated.
| | Sample_growth_protocol_ch1 | For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).
| | Sample_hyb_protocol | RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Chips were scanned on a GeneArray scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Olcay,,Batuman
| | Sample_contact_institute | SUNY Downstate Medical Center
| | Sample_contact_address | 450 Clarkson Ave, Box 20
| | Sample_contact_city | Brooklyn
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 11203
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM700nnn/GSM700587/suppl/GSM700587.CEL.gz
| | Sample_series_id | GSE28327
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700588 | GPL570 |
|
Myeloma tumor, sample 8
|
Bone marrow, tumor cells, MM
|
tissue: bone marrow
cell type: CD138+ tumor plasma cells
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_TUMOR_08
Newly diagnosed patient.
|
| Sample_geo_accession | GSM700588
| | Sample_status | Public on Apr 02 2011
| | Sample_submission_date | Apr 01 2011
| | Sample_last_update_date | Apr 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were untreated.
| | Sample_growth_protocol_ch1 | For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).
| | Sample_hyb_protocol | RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Chips were scanned on a GeneArray scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Olcay,,Batuman
| | Sample_contact_institute | SUNY Downstate Medical Center
| | Sample_contact_address | 450 Clarkson Ave, Box 20
| | Sample_contact_city | Brooklyn
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 11203
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM700nnn/GSM700588/suppl/GSM700588.CEL.gz
| | Sample_series_id | GSE28327
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700589 | GPL570 |
|
Myeloma tumor, sample 9
|
Bone marrow, tumor cells, MM
|
tissue: bone marrow
cell type: CD138+ tumor plasma cells
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_TUMOR_09
Newly diagnosed patient.
|
| Sample_geo_accession | GSM700589
| | Sample_status | Public on Apr 02 2011
| | Sample_submission_date | Apr 01 2011
| | Sample_last_update_date | Apr 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were untreated.
| | Sample_growth_protocol_ch1 | For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).
| | Sample_hyb_protocol | RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Chips were scanned on a GeneArray scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Olcay,,Batuman
| | Sample_contact_institute | SUNY Downstate Medical Center
| | Sample_contact_address | 450 Clarkson Ave, Box 20
| | Sample_contact_city | Brooklyn
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 11203
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM700nnn/GSM700589/suppl/GSM700589.CEL.gz
| | Sample_series_id | GSE28327
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700590 | GPL570 |
|
Myeloma tumor, sample 10
|
Bone marrow, tumor cells, MM
|
tissue: bone marrow
cell type: CD138+ tumor plasma cells
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_TUMOR_10
Newly diagnosed patient.
|
| Sample_geo_accession | GSM700590
| | Sample_status | Public on Apr 02 2011
| | Sample_submission_date | Apr 01 2011
| | Sample_last_update_date | Apr 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were untreated.
| | Sample_growth_protocol_ch1 | For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).
| | Sample_hyb_protocol | RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Chips were scanned on a GeneArray scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Olcay,,Batuman
| | Sample_contact_institute | SUNY Downstate Medical Center
| | Sample_contact_address | 450 Clarkson Ave, Box 20
| | Sample_contact_city | Brooklyn
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 11203
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM700nnn/GSM700590/suppl/GSM700590.CEL.gz
| | Sample_series_id | GSE28327
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700591 | GPL570 |
|
Myeloma tumor, sample 11
|
Bone marrow, tumor cells, MM
|
tissue: bone marrow
cell type: CD138+ tumor plasma cells
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_TUMOR_11
Newly diagnosed patient.
|
| Sample_geo_accession | GSM700591
| | Sample_status | Public on Apr 02 2011
| | Sample_submission_date | Apr 01 2011
| | Sample_last_update_date | Apr 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were untreated.
| | Sample_growth_protocol_ch1 | For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).
| | Sample_hyb_protocol | RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Chips were scanned on a GeneArray scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Olcay,,Batuman
| | Sample_contact_institute | SUNY Downstate Medical Center
| | Sample_contact_address | 450 Clarkson Ave, Box 20
| | Sample_contact_city | Brooklyn
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 11203
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM700nnn/GSM700591/suppl/GSM700591.CEL.gz
| | Sample_series_id | GSE28327
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700592 | GPL570 |
|
Myeloma tumor, sample 12
|
Bone marrow, tumor cells, MM
|
tissue: bone marrow
cell type: CD138+ tumor plasma cells
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_TUMOR_12
Newly diagnosed patient.
|
| Sample_geo_accession | GSM700592
| | Sample_status | Public on Apr 02 2011
| | Sample_submission_date | Apr 01 2011
| | Sample_last_update_date | Apr 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were untreated.
| | Sample_growth_protocol_ch1 | For samples containing <90% tumor plasma cells, CD138-positive tumor cells were enriched by magnetic bead separation (Miltenyi Biotec, Auburn, CA) by collecting non-adherent cells on laminin-coated plates to ensure ≥90% CD38+ by flow cytometry for genomic studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM tumor cells (BD Biosciences, San Jose, CA) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA quality was verified by agarose gel electrophoresis and by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated 3'-labeled RNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2005-2009, Affymetrix).
| | Sample_hyb_protocol | RNA samples were hybridized to individual Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Chips were scanned on a GeneArray scanner (Affymetrix).
| | Sample_data_processing | Affymetrix Microarray Suite version 5.0 was used to quantify digitized image data into raw intensity values for each probe using the GeneChip Operating Software Cell Analysis algorithm (Affymetrix, Santa Clara, CA). Affymetrix .CEL files containing raw probe intensity values from MM tumor cells were analyzed using GeneSpring GX 7.3 software (Agilent Technologies). Probes were summarized into probe sets for each transcript represented on the chip using Robust Multi-Chip Average background adjustment, quantile normalization, and summarization in the manner of Irizarry et al. (Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15.).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Olcay,,Batuman
| | Sample_contact_institute | SUNY Downstate Medical Center
| | Sample_contact_address | 450 Clarkson Ave, Box 20
| | Sample_contact_city | Brooklyn
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 11203
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM700nnn/GSM700592/suppl/GSM700592.CEL.gz
| | Sample_series_id | GSE28327
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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