Search results for the GEO ID: GSE27838  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM687236 | GPL570 |
|
NK_Donor_11
|
enriched non-expanded natural killer cells from healthy donor
|
individual: Donor 11
cell type: natural killer cells
nkc state: non-expanded
|
HD_NK_11
Gene expression data from donor non-expanded NK cells
|
| Sample_geo_accession | GSM687236
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687236/suppl/GSM687236.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687237 | GPL570 |
|
NK_Donor_12
|
enriched non-expanded natural killer cells from healthy donor
|
individual: Donor 12
cell type: natural killer cells
nkc state: non-expanded
|
HD_NK_12
Gene expression data from donor non-expanded NK cells
|
| Sample_geo_accession | GSM687237
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687237/suppl/GSM687237.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687238 | GPL570 |
|
NK_Donor_13
|
enriched non-expanded natural killer cells from healthy donor
|
individual: Donor 13
cell type: natural killer cells
nkc state: non-expanded
|
HD_NK_13
Gene expression data from donor non-expanded NK cells
|
| Sample_geo_accession | GSM687238
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687238/suppl/GSM687238.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687239 | GPL570 |
|
NK_Donor_14
|
enriched non-expanded natural killer cells from healthy donor
|
individual: Donor 14
cell type: natural killer cells
nkc state: non-expanded
|
HD_NK_14
Gene expression data from donor non-expanded NK cells
|
| Sample_geo_accession | GSM687239
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687239/suppl/GSM687239.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687240 | GPL570 |
|
NK_Donor_16
|
enriched non-expanded natural killer cells from healthy donor
|
individual: Donor 16
cell type: natural killer cells
nkc state: non-expanded
|
HD_NK_16
Gene expression data from donor non-expanded NK cells
|
| Sample_geo_accession | GSM687240
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687240/suppl/GSM687240.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687241 | GPL570 |
|
NK_Donor_17
|
enriched non-expanded natural killer cells from healthy donor
|
individual: Donor 17
cell type: natural killer cells
nkc state: non-expanded
|
HD_NK_17
Gene expression data from donor non-expanded NK cells
|
| Sample_geo_accession | GSM687241
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687241/suppl/GSM687241.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687242 | GPL570 |
|
NK_Donor_18
|
enriched non-expanded natural killer cells from healthy donor
|
individual: Donor 18
cell type: natural killer cells
nkc state: non-expanded
|
HD_NK_18
Gene expression data from donor non-expanded NK cells
|
| Sample_geo_accession | GSM687242
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687242/suppl/GSM687242.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687243 | GPL570 |
|
NK_Donor_19
|
enriched non-expanded natural killer cells from healthy donor
|
individual: Donor 19
cell type: natural killer cells
nkc state: non-expanded
|
HD_NK_19
Gene expression data from donor non-expanded NK cells
|
| Sample_geo_accession | GSM687243
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687243/suppl/GSM687243.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687244 | GPL570 |
|
ENK_Donor_11
|
enriched expanded natural killer cells from healthy donor
|
individual: Donor 11
cell type: natural killer cells
nkc state: expanded
|
HD_ENK_11
Gene expression data from donor expanded NK cells
|
| Sample_geo_accession | GSM687244
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687244/suppl/GSM687244.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687245 | GPL570 |
|
ENK_Donor_12
|
enriched expanded natural killer cells from healthy donor
|
individual: Donor 12
cell type: natural killer cells
nkc state: expanded
|
HD_ENK_12
Gene expression data from donor expanded NK cells
|
| Sample_geo_accession | GSM687245
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687245/suppl/GSM687245.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687246 | GPL570 |
|
ENK_Donor_13
|
enriched expanded natural killer cells from healthy donor
|
individual: Donor 13
cell type: natural killer cells
nkc state: expanded
|
HD_ENK_13
Gene expression data from donor expanded NK cells
|
| Sample_geo_accession | GSM687246
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687246/suppl/GSM687246.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687247 | GPL570 |
|
ENK_Donor_14
|
enriched expanded natural killer cells from healthy donor
|
individual: Donor 14
cell type: natural killer cells
nkc state: expanded
|
HD_ENK_14
Gene expression data from donor expanded NK cells
|
| Sample_geo_accession | GSM687247
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687247/suppl/GSM687247.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687248 | GPL570 |
|
ENK_Donor_16
|
enriched expanded natural killer cells from healthy donor
|
individual: Donor 16
cell type: natural killer cells
nkc state: expanded
|
HD_ENK_16
Gene expression data from donor expanded NK cells
|
| Sample_geo_accession | GSM687248
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687248/suppl/GSM687248.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687249 | GPL570 |
|
ENK_Donor_17
|
enriched expanded natural killer cells from healthy donor
|
individual: Donor 17
cell type: natural killer cells
nkc state: expanded
|
HD_ENK_17
Gene expression data from donor expanded NK cells
|
| Sample_geo_accession | GSM687249
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687249/suppl/GSM687249.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687250 | GPL570 |
|
ENK_Donor_18
|
enriched expanded natural killer cells from healthy donor
|
individual: Donor 18
cell type: natural killer cells
nkc state: expanded
|
HD_ENK_18
Gene expression data from donor expanded NK cells
|
| Sample_geo_accession | GSM687250
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687250/suppl/GSM687250.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687251 | GPL570 |
|
ENK_Donor_19
|
enriched expanded natural killer cells from healthy donor
|
individual: Donor 19
cell type: natural killer cells
nkc state: expanded
|
HD_ENK_19
Gene expression data from donor expanded NK cells
|
| Sample_geo_accession | GSM687251
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687251/suppl/GSM687251.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687252 | GPL570 |
|
NK_myeloma_patient_14
|
enriched non-expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 14
cell type: natural killer cells
nkc state: non-expanded
|
MM_NK_14
Gene expression data from myeloma patient non-expanded NK cells
|
| Sample_geo_accession | GSM687252
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687252/suppl/GSM687252.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687253 | GPL570 |
|
NK_myeloma_patient_15
|
enriched non-expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 15
cell type: natural killer cells
nkc state: non-expanded
|
MM_NK_15
Gene expression data from myeloma patient non-expanded NK cells
|
| Sample_geo_accession | GSM687253
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687253/suppl/GSM687253.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687254 | GPL570 |
|
NK_myeloma_patient_16
|
enriched non-expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 16
cell type: natural killer cells
nkc state: non-expanded
|
MM_NK_16
Gene expression data from myeloma patient non-expanded NK cells
|
| Sample_geo_accession | GSM687254
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687254/suppl/GSM687254.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687255 | GPL570 |
|
NK_myeloma_patient_17
|
enriched non-expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 17
cell type: natural killer cells
nkc state: non-expanded
|
MM_NK_17
Gene expression data from myeloma patient non-expanded NK cells
|
| Sample_geo_accession | GSM687255
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687255/suppl/GSM687255.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687256 | GPL570 |
|
NK_myeloma_patient_18
|
enriched non-expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 18
cell type: natural killer cells
nkc state: non-expanded
|
MM_NK_18
Gene expression data from myeloma patient non-expanded NK cells
|
| Sample_geo_accession | GSM687256
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687256/suppl/GSM687256.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687257 | GPL570 |
|
NK_myeloma_patient_19
|
enriched non-expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 19
cell type: natural killer cells
nkc state: non-expanded
|
MM_NK_19
Gene expression data from myeloma patient non-expanded NK cells
|
| Sample_geo_accession | GSM687257
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687257/suppl/GSM687257.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687258 | GPL570 |
|
NK_myeloma_patient_20
|
enriched non-expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 20
cell type: natural killer cells
nkc state: non-expanded
|
MM_NK_20
Gene expression data from myeloma patient non-expanded NK cells
|
| Sample_geo_accession | GSM687258
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687258/suppl/GSM687258.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687259 | GPL570 |
|
NK_myeloma_patient_24
|
enriched non-expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 24
cell type: natural killer cells
nkc state: non-expanded
|
MM_NK_24
Gene expression data from myeloma patient non-expanded NK cells
|
| Sample_geo_accession | GSM687259
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687259/suppl/GSM687259.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687260 | GPL570 |
|
ENK_myeloma_patient_14
|
enriched expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 14
cell type: natural killer cells
nkc state: expanded
|
MM_ENK_14
Gene expression data from myeloma patient expanded NK cells
|
| Sample_geo_accession | GSM687260
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687260/suppl/GSM687260.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687261 | GPL570 |
|
ENK_myeloma_patient_15
|
enriched expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 15
cell type: natural killer cells
nkc state: expanded
|
MM_ENK_15
Gene expression data from myeloma patient expanded NK cells
|
| Sample_geo_accession | GSM687261
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687261/suppl/GSM687261.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687262 | GPL570 |
|
ENK_myeloma_patient_16
|
enriched expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 16
cell type: natural killer cells
nkc state: expanded
|
MM_ENK_16
Gene expression data from myeloma patient expanded NK cells
|
| Sample_geo_accession | GSM687262
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687262/suppl/GSM687262.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687263 | GPL570 |
|
ENK_myeloma_patient_17
|
enriched expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 17
cell type: natural killer cells
nkc state: expanded
|
MM_ENK_17
Gene expression data from myeloma patient expanded NK cells
|
| Sample_geo_accession | GSM687263
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687263/suppl/GSM687263.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687264 | GPL570 |
|
ENK_myeloma_patient_18
|
enriched expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 18
cell type: natural killer cells
nkc state: expanded
|
MM_ENK_18
Gene expression data from myeloma patient expanded NK cells
|
| Sample_geo_accession | GSM687264
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687264/suppl/GSM687264.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687265 | GPL570 |
|
ENK_myeloma_patient_19
|
enriched expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 19
cell type: natural killer cells
nkc state: expanded
|
MM_ENK_19
Gene expression data from myeloma patient expanded NK cells
|
| Sample_geo_accession | GSM687265
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687265/suppl/GSM687265.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687266 | GPL570 |
|
ENK_myeloma_patient_20
|
enriched expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 20
cell type: natural killer cells
nkc state: expanded
|
MM_ENK_20
Gene expression data from myeloma patient expanded NK cells
|
| Sample_geo_accession | GSM687266
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687266/suppl/GSM687266.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
GSM687267 | GPL570 |
|
ENK_myeloma_patient_24
|
enriched expanded natural killer cells from myeloma patient
|
individual: Myeloma patient 24
cell type: natural killer cells
nkc state: expanded
|
MM_ENK_24
Gene expression data from myeloma patient expanded NK cells
|
| Sample_geo_accession | GSM687267
| | Sample_status | Public on Mar 08 2011
| | Sample_submission_date | Mar 08 2011
| | Sample_last_update_date | Mar 08 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
| | Sample_growth_protocol_ch1 | NK Enrichment Protocol: NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells. For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. Scanned images were processed using the GCOS v1.4 software.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tarun,Kumar,Garg
| | Sample_contact_email | gargtarunk@uams.edu
| | Sample_contact_phone | 501-526-6990-8482
| | Sample_contact_laboratory | Immunotherapy Lab
| | Sample_contact_department | Myeloma Institute for Research and Therapy
| | Sample_contact_institute | University of Arkansas for Medical Sciences
| | Sample_contact_address | 4301 W Markham St
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM687nnn/GSM687267/suppl/GSM687267.CEL.gz
| | Sample_series_id | GSE27838
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
