Search results for the GEO ID: GSE28326  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM700561 | GPL570 |
|
Myeloma EPC, sample 1
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_EPC_01
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700561
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700561/suppl/GSM700561.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700562 | GPL570 |
|
Myeloma EPC, sample 2
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_EPC_02
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700562
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700562/suppl/GSM700562.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700563 | GPL570 |
|
Myeloma EPC, sample 3
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_EPC_03
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700563
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700563/suppl/GSM700563.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700564 | GPL570 |
|
Myeloma EPC, sample 4
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_EPC_04
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700564
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700564/suppl/GSM700564.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700565 | GPL570 |
|
Myeloma EPC, sample 5
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_EPC_05
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700565
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700565/suppl/GSM700565.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700566 | GPL570 |
|
Myeloma EPC, sample 6
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_EPC_06
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700566
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700566/suppl/GSM700566.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700567 | GPL570 |
|
Myeloma EPC, sample 7
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_EPC_07
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700567
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700567/suppl/GSM700567.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700568 | GPL570 |
|
Myeloma EPC, sample 8
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_EPC_08
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700568
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700568/suppl/GSM700568.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700569 | GPL570 |
|
Myeloma EPC, sample 9
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_EPC_09
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700569
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700569/suppl/GSM700569.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700570 | GPL570 |
|
Myeloma EPC, sample 10
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_EPC_10
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700570
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700570/suppl/GSM700570.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700571 | GPL570 |
|
Myeloma EPC, sample 11
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_EPC_11
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700571
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700571/suppl/GSM700571.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700572 | GPL570 |
|
Myeloma EPC, sample 12
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_EPC_12
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700572
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700572/suppl/GSM700572.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700573 | GPL570 |
|
Myeloma EPC, sample 13
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_EPC_13
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700573
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700573/suppl/GSM700573.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700574 | GPL570 |
|
Myeloma EPC, sample 14
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_EPC_14
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700574
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700574/suppl/GSM700574.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700575 | GPL570 |
|
Myeloma EPC, sample 15
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_EPC_15
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700575
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700575/suppl/GSM700575.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700576 | GPL570 |
|
Myeloma EPC, sample 16
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_EPC_16
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700576
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700576/suppl/GSM700576.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700577 | GPL570 |
|
Myeloma EPC, sample 17
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_EPC_17
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700577
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700577/suppl/GSM700577.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700578 | GPL570 |
|
Myeloma EPC, sample 18
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: male
disease state: advanced multiple myeloma (MM)
|
MM_EPC_18
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700578
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700578/suppl/GSM700578.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700579 | GPL570 |
|
Myeloma EPC, sample 19
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_EPC_19
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700579
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700579/suppl/GSM700579.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
GSM700580 | GPL570 |
|
Myeloma EPC, sample 20
|
Bone marrow, EPC, MM
|
tissue: bone marrow
cell type: endothelial progenitor cell (EPC)
gender: female
disease state: advanced multiple myeloma (MM)
|
MM_EPC_20
Newly diagnosed MM patient.
|
| Sample_geo_accession | GSM700580
| | 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 | EPCs were obtained by Ficoll-Hypaque (Sigma Chemicals, St. Louis, MO) density-gradient centrifugation within 6 hours of collection of bone marrow aspirates, and the 138-negative (Miltenyi Biotec) mononuclear cell layer was resuspended in EndoCult Basal Medium supplemented with 20% fetal bovine serum (StemCell Technologies, Vancouver, Canada) and antibiotics (100 U/ml penicillin G, 100 μg/ml streptomycin). To eliminate contamination with mature ECs and other adherent BM cells, the mononuclear cells (7 × 10^6/well) were plated overnight in laminin-coated, 6-well plates (Becton Dickinson Labware, Bedford, MA), and non-adherent EPCs were collected and plated in 25 cm2 laminin-coated flasks. Under these culture conditions, characteristic EPC colonies are observed at 5-7 days, and confluence is reached 10-14 days after plating. EPC enrichment was quantitated by growing EPCs in parallel on laminin-coated, 96-well plates (Becton Dickinson Labware) and immunostaining with combinations of antibodies directed against EPC markers, VEGFR-2, CD133, CD144 (vascular endothelial cadherin [VE-cadherin]), and von Willebrand factor (vWF), without evidence of plasma cell (CD38), lymphocyte (CD45), and monocyte (CD11b) contamination and was >98%. To minimize culture-induced genomic changes, only first-passage EPCs were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA (15 μg) for microarrays was extracted independently from 6 X 10^6 MM EPCs 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 EPCs 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/GSM700580/suppl/GSM700580.CEL.gz
| | Sample_series_id | GSE28326
| | Sample_series_id | GSE28331
| | Sample_data_row_count | 54675
| | |
|
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