Search results for the GEO ID: GSE9241  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM234706 | GPL8300 |
|
DC_1_CT0hr
|
dendritic cells, control, 0 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the -catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234706
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | For this sample, clusters of Langerhans cells were harvested at 0 hours for microarray analysis.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 104 U/mg), 2.5 ng/ml TNF- (2 x 107 U/mg), 0.5 ng/ml TGF-ß1 (2 x 107 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234706/suppl/GSM234706.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234706/suppl/GSM234706.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234708 | GPL8300 |
|
DC_2_CT36hr
|
dendritic cells, control, 36 hours
|
Human Langerhans cells produced from CD34+ stem cells cultured as described in the Growth Protocol section, were incubated for 36 hours without maturation stimulus.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the -catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234708
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | For this sample, clusters of Langerhans cells were harvested at 36 hours for microarray analysis.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234708/suppl/GSM234708.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234708/suppl/GSM234708.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234710 | GPL8300 |
|
DC_3_CD1hr
|
dendritic cells, cluster disruption, 1 hour
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the -catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234710
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | For this sample, clusters of Langerhans cells were disrupted with repetitive pipeting, and harvested at 1 hour for microarray analysis.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234710/suppl/GSM234710.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234710/suppl/GSM234710.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234712 | GPL8300 |
|
DC_4_CD3hr
|
dendritic cells, cluster disruption, 3 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234712
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | For this sample, clusters of Langerhans cells were disrupted with repetitive pipeting, and harvested 3 hours later for microarray analysis.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234712/suppl/GSM234712.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234712/suppl/GSM234712.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234713 | GPL8300 |
|
DC_5_CD6hr
|
dendritic cells, cluster disruption, 6 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234713
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | For this sample, clusters of Langerhans cells were disrupted with repetitive pipeting, and harvested 6 hours later for microarray analysis.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234713/suppl/GSM234713.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234713/suppl/GSM234713.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234716 | GPL8300 |
|
DC_6_CD12hr
|
dendritic cells, cluster disruption, 12 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234716
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | For this sample, clusters of Langerhans cells were disrupted with repetitive pipeting, and harvested 12 hours later for microarray analysis.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234716/suppl/GSM234716.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234716/suppl/GSM234716.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234717 | GPL8300 |
|
DC_7_CD18hr
|
dendritic cells, cluster disruption, 18 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234717
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | For this sample, clusters of Langerhans cells were disrupted with repetitive pipeting, and harvested 18 hours later for microarray analysis.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234717/suppl/GSM234717.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234717/suppl/GSM234717.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234718 | GPL8300 |
|
DC_8_CD36hr
|
dendritic cells, cluster disruption, 36 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234718
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | For this sample, clusters of Langerhans cells were disrupted with repetitive pipeting, and harvested 36 hours later for microarray analysis.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234718/suppl/GSM234718.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234718/suppl/GSM234718.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234719 | GPL8300 |
|
DC_9_B1hr
|
dendritic cells, stimulated by bacteria, 1 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234719
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | Clusters of Langerhans cells, grown as described in the Growth Protocol section, were stimulated to mature with the addition of additional bacterial (DH5alpha) or LPS (250 ng/ml). For this sample, cells were harvested for microarray analysis after one hour of treatment.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234719/suppl/GSM234719.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234719/suppl/GSM234719.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234720 | GPL8300 |
|
DC_10_B3hr
|
dendritic cells, stimulated by bacteria, 3 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234720
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | Clusters of Langerhans cells, grown as described in the Growth Protocol section, were stimulated to mature with the addition of additional bacterial (DH5alpha) or LPS (250 ng/ml). For this sample, cells were harvested for microarray analysis after 3 hours of treatment.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234720/suppl/GSM234720.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234720/suppl/GSM234720.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234722 | GPL8300 |
|
DC_11_B6hr
|
dendritic cells, stimulated by bacteria, 6 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234722
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | Clusters of Langerhans cells, grown as described in the Growth Protocol section, were stimulated to mature with the addition of additional bacterial (DH5alpha) or LPS (250 ng/ml). For this sample, cells were harvested for microarray analysis after 6 hours of treatment.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234722/suppl/GSM234722.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234722/suppl/GSM234722.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234723 | GPL8300 |
|
DC_12_B12hr
|
dendritic cells, stimulated by bacteria, 12 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234723
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | Clusters of Langerhans cells, grown as described in the Growth Protocol section, were stimulated to mature with the addition of additional bacterial (DH5alpha) or LPS (250 ng/ml). For this sample, cells were harvested for microarray analysis after 12 hours of treatment.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234723/suppl/GSM234723.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234723/suppl/GSM234723.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234757 | GPL8300 |
|
DC_13_B18hr
|
dendritic cells, stimulated by bacteria, 18 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234757
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | Clusters of Langerhans cells, grown as described in the Growth Protocol section, were stimulated to mature with the addition of additional bacterial (DH5alpha) or LPS (250 ng/ml). For this sample, cells were harvested for microarray analysis after 18 hours of treatment.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234757/suppl/GSM234757.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234757/suppl/GSM234757.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234758 | GPL8300 |
|
DC_14_B36hr
|
dendritic cells, stimulated by bacteria, 36 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234758
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | Clusters of Langerhans cells, grown as described in the Growth Protocol section, were stimulated to mature with the addition of additional bacterial (DH5alpha) or LPS (250 ng/ml). For this sample, cells were harvested for microarray analysis after 36 hours of treatment.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234758/suppl/GSM234758.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234758/suppl/GSM234758.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234760 | GPL8300 |
|
DC_15_Ab6hr
|
dendritic cells, cluster disruption and Anti E-cadherin, 6 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234760
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | Clusters of Langerhans cells were treated with 5 ug/ml of anti-human E-cadherin antibody prior to disruption with repetitive pipeting. Samples were harvested 6 hours later for microarray analysis.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234760/suppl/GSM234760.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234760/suppl/GSM234760.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
| | |
|
GSM234761 | GPL8300 |
|
DC_16_Ab12hr
|
dendritic cells, cluster disruption and Anti E-cadherin, 12 hours
|
Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
|
The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
|
| Sample_geo_accession | GSM234761
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | Clusters of Langerhans cells were treated with 5 ug/ml of anti-human E-cadherin antibody prior to disruption with repetitive pipeting. Samples were harvested 12 hours later for microarray analysis.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234761/suppl/GSM234761.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234761/suppl/GSM234761.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
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GSM234762 | GPL8300 |
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DC_17_Ab36hr
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dendritic cells, cluster disruption and Anti E-cadherin, 36 hours
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Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.
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The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response. We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors. These events were triggered at least in part by activation of the beta-catenin pathway. However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
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| Sample_geo_accession | GSM234762
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Blood Bank, Department of Laboratory Medicine (Yale University School of Medicine)
| | Sample_treatment_protocol_ch1 | Clusters of Langerhans cells were treated with 5 ug/ml of anti-human E-cadherin antibody prior to disruption with repetitive pipeting. Samples were harvested 36 hours later for microarray analysis.
| | Sample_growth_protocol_ch1 | CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies. For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions. Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.
| | Sample_hyb_protocol | Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.
| | Sample_scan_protocol | Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.
| | Sample_data_processing | Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.
| | Sample_platform_id | GPL8300
| | Sample_contact_name | James,Andrew,Whitney
| | Sample_contact_email | awhitney@cgipharma.com
| | Sample_contact_institute | CGI Pharmaceuticals Inc.
| | Sample_contact_address | 36 East Industrial Road
| | Sample_contact_city | Branford
| | Sample_contact_state | CT
| | Sample_contact_zip/postal_code | 06405
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234762/suppl/GSM234762.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234762/suppl/GSM234762.CHP.gz
| | Sample_series_id | GSE9241
| | Sample_data_row_count | 12625
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