Search results for the GEO ID: GSE41889  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1026969 | GPL570 |
|
Freshly isolated monocytes used as MV donors, repl. 1
|
Monocytes
|
cell group: primary
cell type: Monocytes
treatment: primary monocytes
|
Gene expression in primary monocytes
|
| Sample_geo_accession | GSM1026969
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026969/suppl/GSM1026969_NI-Mono-1.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026970 | GPL570 |
|
Freshly isolated monocytes used as MV donors, repl. 2
|
Monocytes
|
cell group: primary
cell type: Monocytes
treatment: primary monocytes
|
Gene expression in primary monocytes
|
| Sample_geo_accession | GSM1026970
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026970/suppl/GSM1026970_NI-Mono-2.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026971 | GPL570 |
|
Freshly isolated monocytes used as MV donors, repl. 3
|
Monocytes
|
cell group: primary
cell type: Monocytes
treatment: primary monocytes
|
Gene expression in primary monocytes
|
| Sample_geo_accession | GSM1026971
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026971/suppl/GSM1026971_NI-Mono-3.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026972 | GPL570 |
|
GM-CSF-treated macrophages used as MV donors, repl. 1
|
Monocyte-derived macrophages
|
cell group: primary
cell type: Monocyte-derived macrophages
treatment: differentiated MDM
|
Gene expression in differentiated MDM
|
| Sample_geo_accession | GSM1026972
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026972/suppl/GSM1026972_NI-GM1.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026973 | GPL570 |
|
GM-CSF-treated macrophages used as MV donors, repl. 2
|
Monocyte-derived macrophages
|
cell group: primary
cell type: Monocyte-derived macrophages
treatment: differentiated MDM
|
Gene expression in differentiated MDM
|
| Sample_geo_accession | GSM1026973
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026973/suppl/GSM1026973_NI-GM2.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026974 | GPL570 |
|
GM-CSF-treated macrophages used as MV donors, repl. 3
|
Monocyte-derived macrophages
|
cell group: primary
cell type: Monocyte-derived macrophages
treatment: differentiated MDM
|
Gene expression in differentiated MDM
|
| Sample_geo_accession | GSM1026974
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026974/suppl/GSM1026974_NI-GM3.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026975 | GPL570 |
|
Freshly isolated monocytes used as MV recipients, repl. 1
|
Monocytes
|
cell group: primary
cell type: Monocytes
treatment: differentiated MDM
|
Gene expression in differentiated MDM
|
| Sample_geo_accession | GSM1026975
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026975/suppl/GSM1026975_CM-BC-1.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026976 | GPL570 |
|
Freshly isolated monocytes used as MV recipients, repl. 2
|
Monocytes
|
cell group: primary
cell type: Monocytes
treatment: differentiated MDM
|
Gene expression in differentiated MDM
|
| Sample_geo_accession | GSM1026976
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026976/suppl/GSM1026976_CM-BC-2.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026977 | GPL570 |
|
Freshly isolated monocytes used as MV recipients, repl. 3
|
Monocytes
|
cell group: primary
cell type: Monocytes
treatment: differentiated MDM
|
Gene expression in differentiated MDM
|
| Sample_geo_accession | GSM1026977
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026977/suppl/GSM1026977_CM-BC-3.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026978 | GPL570 |
|
Freshly isolated monocyte incubated 24 h with MV from other GM-CSF-treated MDM, repl. 1
|
Monocyte-derived macrophages
|
cell group: primary
cell type: Monocyte-derived macrophages
treatment: MDM after interaction with MDM-derived MV
|
Gene expression in MDM after interaction with MDM-derived MV
|
| Sample_geo_accession | GSM1026978
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026978/suppl/GSM1026978_CM-BC-GMCSF-MV24-1.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026979 | GPL570 |
|
Freshly isolated monocyte incubated 24 h with MV from other GM-CSF-treated MDM, repl. 2
|
Monocyte-derived macrophages
|
cell group: primary
cell type: Monocyte-derived macrophages
treatment: MDM after interaction with MDM-derived MV
|
Gene expression in MDM after interaction with MDM-derived MV
|
| Sample_geo_accession | GSM1026979
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026979/suppl/GSM1026979_CM-BC-GMCSF-MV24-2.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026980 | GPL570 |
|
Freshly isolated monocyte incubated 24 h with MV from other GM-CSF-treated MDM, repl. 3
|
Monocyte-derived macrophages
|
cell group: primary
cell type: Monocyte-derived macrophages
treatment: MDM after interaction with MDM-derived MV
|
Gene expression in MDM after interaction with MDM-derived MV
|
| Sample_geo_accession | GSM1026980
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026980/suppl/GSM1026980_CM-BC-GMCSF-MV24-3.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026981 | GPL570 |
|
THP1+DMSO used as MV donors, repl. 1
|
THP1 cells
|
cell group: cell line
cell type: THP1 cells
treatment: THP1 cells treated with DMSO
|
Gene expression in THP1 cells treated with DMSO
|
| Sample_geo_accession | GSM1026981
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026981/suppl/GSM1026981_CM-DMSO-1.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026982 | GPL570 |
|
THP1+DMSO used as MV donors, repl. 2
|
THP1 cells
|
cell group: cell line
cell type: THP1 cells
treatment: THP1 cells treated with DMSO
|
Gene expression in THP1 cells treated with DMSO
|
| Sample_geo_accession | GSM1026982
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026982/suppl/GSM1026982_CM-DMSO-2.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026983 | GPL570 |
|
THP1+DMSO used as MV donors, repl. 3
|
THP1 cells
|
cell group: cell line
cell type: THP1 cells
treatment: THP1 cells treated with DMSO
|
Gene expression in THP1 cells treated with DMSO
|
| Sample_geo_accession | GSM1026983
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026983/suppl/GSM1026983_CM-DMSO-3.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026984 | GPL570 |
|
THP1 incubated 24 h with MV from THP1-DMSO donors, repl. 1
|
THP1 cells
|
cell group: cell line
cell type: THP1 cells
treatment: THP1 cells treated with THP1+DMSO-derived MV
|
Gene expression in THP1 cells treated with THP1+DMSO-derived MV
|
| Sample_geo_accession | GSM1026984
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026984/suppl/GSM1026984_CM-DMSO-MV24-1.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026985 | GPL570 |
|
THP1 incubated 24 h with MV from THP1-DMSO donors, repl. 2
|
THP1 cells
|
cell group: cell line
cell type: THP1 cells
treatment: THP1 cells treated with THP1+DMSO-derived MV
|
Gene expression in THP1 cells treated with THP1+DMSO-derived MV
|
| Sample_geo_accession | GSM1026985
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026985/suppl/GSM1026985_CM-DMSO-MV24-2.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026986 | GPL570 |
|
THP1 incubated 24 h with MV from THP1-DMSO donors, repl. 3
|
THP1 cells
|
cell group: cell line
cell type: THP1 cells
treatment: THP1 cells treated with THP1+DMSO-derived MV
|
Gene expression in THP1 cells treated with THP1+DMSO-derived MV
|
| Sample_geo_accession | GSM1026986
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026986/suppl/GSM1026986_CM-DMSO-MV24-3.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026987 | GPL570 |
|
THP1+PMA used as MV donors, repl. 1
|
THP1 cells
|
cell group: cell line
cell type: THP1 cells
treatment: THP1 cells treated with PMA
|
Gene expression in THP1 cells treated with PMA
|
| Sample_geo_accession | GSM1026987
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026987/suppl/GSM1026987_CM-PMA-1.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026988 | GPL570 |
|
THP1+PMA used as MV donors, repl. 2
|
THP1 cells
|
cell group: cell line
cell type: THP1 cells
treatment: THP1 cells treated with PMA
|
Gene expression in THP1 cells treated with PMA
|
| Sample_geo_accession | GSM1026988
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026988/suppl/GSM1026988_CM-PMA-2.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026989 | GPL570 |
|
THP1+PMA used as MV donors, repl. 3
|
THP1 cells
|
cell group: cell line
cell type: THP1 cells
treatment: THP1 cells treated with PMA
|
Gene expression in THP1 cells treated with PMA
|
| Sample_geo_accession | GSM1026989
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026989/suppl/GSM1026989_CM-PMA-3.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026990 | GPL570 |
|
THP1 incubated 24 h with MV from THP1-PMA donors, repl. 1
|
THP1 cells
|
cell group: cell line
cell type: THP1 cells
treatment: THP1 cells treated with THP1+PMA-derived MV
|
Gene expression in THP1 cells treated with THP1+PMA-derived MV
|
| Sample_geo_accession | GSM1026990
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026990/suppl/GSM1026990_CM-PMA-MV24-1.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026991 | GPL570 |
|
THP1 incubated 24 h with MV from THP1-PMA donors, repl. 2
|
THP1 cells
|
cell group: cell line
cell type: THP1 cells
treatment: THP1 cells treated with THP1+PMA-derived MV
|
Gene expression in THP1 cells treated with THP1+PMA-derived MV
|
| Sample_geo_accession | GSM1026991
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026991/suppl/GSM1026991_CM-PMA-MV24-2.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
|
GSM1026992 | GPL570 |
|
THP1 incubated 24 h with MV from THP1-PMA donors, repl. 3
|
THP1 cells
|
cell group: cell line
cell type: THP1 cells
treatment: THP1 cells treated with THP1+PMA-derived MV
|
Gene expression in THP1 cells treated with THP1+PMA-derived MV
|
| Sample_geo_accession | GSM1026992
| | Sample_status | Public on Mar 08 2013
| | Sample_submission_date | Oct 28 2012
| | Sample_last_update_date | Mar 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Microvesicles (MV) were obtained by a 30 min, 4°C, 16000 x g centrifugation of the cell-free culture supernatant. Primary monocyte-derived macrophages were treated either with GM-CSF or with MV derived from other GM-CSF-treated macrophages, for 24 h. THP1 cells were treated with PMA or DMSO (control). MV were isolated from these cells and further incubated for 24 h with new THP1 cells.
| | Sample_growth_protocol_ch1 | Peripheral human blood monocytes were isolated from buffy coats, on histopaque-1077, and grown in X-VIVO 15 media (Lonza) supplemented with 10 μg/ml polymyxin B, in the absence or presence of 50 ng/ml of rhGM-CSF. Monocytes were washed after 4 hours and cultured in fresh media without added rhGM-CSF. THP-1 cells (ATCC) were grown in RPMI 1640 supplemented with 10% FBS. To induce differentiation, THP-1 cells were grown in X-VIVO 15 serum-free media and treated with 65 nM PMA, or with vehicle (DMSO) as control.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol methodology. At all steps, the quantity and quality of the preparations were controlled using Nanodrop and Experion Automated Electrophoresis System (BioRad).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For samples Mono1-3 and GM1-3, 2 ug of total RNA were processed with GeneChip® HT One-Cycle Target Labeling and Control Kit (Affymetrix). For all other samples, 30 ng RNA were processed using the Ovation™ RNA Amplification. The cDNA thus obtained was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (both kits from NuGEN Technologies, Inc., San Carlos, CA).
| | Sample_hyb_protocol | For samples Mono1-3 and GM1-3, 15ug of biotin labeled cRNA were hybridized to the array, washed and stained in Affymetrix Fluidics Station 450, using protocol EukGE-WS2v5-450. For all other samples, GeneChips were hybridized with 3.75 ug biotin-labeled, fragmented cDNA, then washed and stained in Affymetrix Fluidics Station 400, using protocol EukGE-WS2v5.
| | Sample_scan_protocol | The Affymetrix GeneChip Scanner 7G was used for samples Mono1-3 and GM1-3 and Affymetrix GeneChip Scanner 3000 was used to scan all other samples.
| | Sample_data_processing | Presence call was obtained with GeneChip Operating Software Version 1.4.0.036. Data were processed with Partek Genomic Suite 6.4, after importing from .CEL files using robust multi-chip average with GC content adjustment (GC-RMA) for background correction, and quantile normalization. Only those genes that demonstrated a P (present) or M (marginal) call in at least two experimental samples of the triplicate per experimental conditions were futher used for analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Leni,,Moldovan
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Davis Heart and Lung Research Institute
| | Sample_contact_address | 460 W 12th Ave, BRT Rm. 309
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43210
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1026nnn/GSM1026992/suppl/GSM1026992_CM-PMA-MV24-3.CEL.gz
| | Sample_series_id | GSE41889
| | Sample_data_row_count | 54675
| | |
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