Search results for the GEO ID: GSE11199  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM280331 | GPL570 |
|
LTB1 stim
|
macrophage, ex vivio stimulation TB extract for 4 hrs
|
5 day monocyte-derived macrophage
Latent
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280331
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280331/suppl/GSM280331.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280332 | GPL570 |
|
LTB1 unstim
|
macrophage, ex vivo stimulation with media (control)
|
5 day monocyte-derived macrophage
Latent
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280332
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280332/suppl/GSM280332.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280333 | GPL570 |
|
PTB3 stim
|
macrophage, ex vivio stimulation TB extract for 4 hrs
|
5 day monocyte-derived macrophage
Pulmonary
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280333
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280333/suppl/GSM280333.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280334 | GPL570 |
|
PTB3 unstim
|
macrophage, ex vivo stimulation with media (control)
|
5 day monocyte-derived macrophage
Pulmonary
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280334
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280334/suppl/GSM280334.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280335 | GPL570 |
|
TBM2 stim
|
macrophage, ex vivio stimulation TB extract for 4 hrs
|
5 day monocyte-derived macrophage
meningeal tuberculosis
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280335
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280335/suppl/GSM280335.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280336 | GPL570 |
|
TBM2 unstim
|
macrophage, ex vivo stimulation with media (control)
|
5 day monocyte-derived macrophage
meningeal tuberculosis
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280336
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280336/suppl/GSM280336.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280337 | GPL570 |
|
LTB2 stim
|
macrophage, ex vivio stimulation TB extract for 4 hrs
|
5 day monocyte-derived macrophage
Latent
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280337
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280337/suppl/GSM280337.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280338 | GPL570 |
|
LTB2 unstim
|
macrophage, ex vivo stimulation with media (control)
|
5 day monocyte-derived macrophage
Latent
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280338
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280338/suppl/GSM280338.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280339 | GPL570 |
|
PTB1 stim
|
macrophage, ex vivio stimulation TB extract for 4 hrs
|
5 day monocyte-derived macrophage
Pulmonary
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280339
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280339/suppl/GSM280339.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280340 | GPL570 |
|
PTB1 unstim
|
macrophage, ex vivo stimulation with media (control)
|
5 day monocyte-derived macrophage
Pulmonary
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280340
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280340/suppl/GSM280340.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280341 | GPL570 |
|
TBM3 stim
|
macrophage, ex vivio stimulation TB extract for 4 hrs
|
5 day monocyte-derived macrophage
meningeal tuberculosis
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280341
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280341/suppl/GSM280341.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280342 | GPL570 |
|
TBM3 unstim
|
macrophage, ex vivo stimulation with media (control)
|
5 day monocyte-derived macrophage
meningeal tuberculosis
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280342
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280342/suppl/GSM280342.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280343 | GPL570 |
|
LTB3 stim
|
macrophage, ex vivio stimulation TB extract for 4 hrs
|
5 day monocyte-derived macrophage
Latent
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280343
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280343/suppl/GSM280343.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280344 | GPL570 |
|
LTB3 unstim
|
macrophage, ex vivo stimulation with media (control)
|
5 day monocyte-derived macrophage
Latent
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280344
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280344/suppl/GSM280344.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280345 | GPL570 |
|
LTB4 stim
|
macrophage, ex vivio stimulation TB extract for 4 hrs
|
5 day monocyte-derived macrophage
Latent
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280345
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280345/suppl/GSM280345.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280346 | GPL570 |
|
LTB4 unstim
|
macrophage, ex vivo stimulation with media (control)
|
5 day monocyte-derived macrophage
Latent
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280346
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280346/suppl/GSM280346.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280347 | GPL570 |
|
PTB2 stim
|
macrophage, ex vivio stimulation TB extract for 4 hrs
|
5 day monocyte-derived macrophage
Pulmonary
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280347
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280347/suppl/GSM280347.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280348 | GPL570 |
|
PTB2 unstim
|
macrophage, ex vivo stimulation with media (control)
|
5 day monocyte-derived macrophage
Pulmonary
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280348
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280348/suppl/GSM280348.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280349 | GPL570 |
|
PTB4 stim
|
macrophage, ex vivio stimulation TB extract for 4 hrs
|
5 day monocyte-derived macrophage
Pulmonary
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280349
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280349/suppl/GSM280349.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280350 | GPL570 |
|
PTB4 unstim
|
macrophage, ex vivo stimulation with media (control)
|
5 day monocyte-derived macrophage
Pulmonary
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280350
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280350/suppl/GSM280350.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280351 | GPL570 |
|
TBM1 stim
|
macrophage, ex vivio stimulation TB extract for 4 hrs
|
5 day monocyte-derived macrophage
meningeal tuberculosis
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280351
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280351/suppl/GSM280351.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
| | |
|
GSM280352 | GPL570 |
|
TBM1 unstim
|
macrophage, ex vivo stimulation with media (control)
|
5 day monocyte-derived macrophage
meningeal tuberculosis
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280352
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280352/suppl/GSM280352.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
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GSM280354 | GPL570 |
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TBM4 unstim
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macrophage, ex vivo stimulation with media (control)
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5 day monocyte-derived macrophage
meningeal tuberculosis
|
Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.
|
| Sample_geo_accession | GSM280354
| | Sample_status | Public on Feb 23 2009
| | Sample_submission_date | Apr 08 2008
| | Sample_last_update_date | Feb 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.
| | Sample_growth_protocol_ch1 | Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual
| | Sample_hyb_protocol | Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip
| | Sample_scan_protocol | Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.
| | Sample_data_processing | Raw CEL intensity data were RMA normalized using R/Bioconductor
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,J,Dunstan
| | Sample_contact_email | sdunstan@oucru.org
| | Sample_contact_phone | 84 8 9241761
| | Sample_contact_fax | 84 8 9238904
| | Sample_contact_department | Hospital for Tropical Diseases
| | Sample_contact_institute | 1. Oxford University Clinical Research Unit
| | Sample_contact_address | 190 Ben Ham Tu, Quan 5
| | Sample_contact_city | Ho Chi Minh City
| | Sample_contact_zip/postal_code | 5
| | Sample_contact_country | Viet Nam
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280354/suppl/GSM280354.CEL.gz
| | Sample_series_id | GSE11199
| | Sample_data_row_count | 54675
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