Search results for the GEO ID: GSE14000  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM349873 | GPL570 |
|
0h_PolyRNA_serie1
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 24th of July 2008. RNA extracted out of day5 MoDCs on the 28th of July 2006.
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM349873
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 10 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Oh, NO LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349873/suppl/GSM349873.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349873/suppl/GSM349873.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM349874 | GPL570 |
|
0h_TotRNA_serie1
|
monocyte-derived dendritic cells
|
Monocytes isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 24th of July 2008. RNA extracted out of day5 MoDCs on the 28th of July 2006.
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM349874
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 10 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Oh, NO LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Polysomal RNA (P | other) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349874/suppl/GSM349874.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349874/suppl/GSM349874.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM349875 | GPL570 |
|
4h_PolyRNA_serie1
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 24th of July 2008. RNA extracted out of day5 MoDCs on the 28th of July 2006.
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM349875
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 10 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349875/suppl/GSM349875.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349875/suppl/GSM349875.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM349876 | GPL570 |
|
4h_TotRNA_serie1
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 24th of July 2008. RNA extracted out of day5 MoDCs on the 28th of July 2006.
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM349876
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 10 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349876/suppl/GSM349876.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349876/suppl/GSM349876.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM349877 | GPL570 |
|
16h_PolyRNA_serie1
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 24th of July 2008. RNA extracted out of day5 MoDCs on the 28th of July 2006.
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM349877
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 10 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349877/suppl/GSM349877.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349877/suppl/GSM349877.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM349878 | GPL570 |
|
16h_TotRNA_serie1
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 24th of July 2008. RNA extracted out of day5 MoDCs on the 28th of July 2006.
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM349878
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 10 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349878/suppl/GSM349878.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349878/suppl/GSM349878.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351527 | GPL570 |
|
0h_PolyRNA_serie2
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 23h of November 2006. RNA extracted out of day5 MoDCs on the 4th of december 2006 (MoDC poly #9, serie 2)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351527
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NO LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351527/suppl/GSM351527.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351527/suppl/GSM351527.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351530 | GPL570 |
|
0h_TotRNA_serie2
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 23rd of November 2006. RNA extracted out of day5 MoDCs on the 4th of December 2006. (MoDC Poly # 9)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351530
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NO LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351530/suppl/GSM351530.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351530/suppl/GSM351530.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351531 | GPL570 |
|
4h_PolyRNA_serie2
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 23rd of November 2006. RNA extracted out of day5 MoDCs on the 4th of December 2006. (MoDC Poly # 9)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351531
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NO LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351531/suppl/GSM351531.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351531/suppl/GSM351531.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351532 | GPL570 |
|
4h_TotRNA_serie2
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 23rd of November 2006. RNA extracted out of day5 MoDCs on the 4th of December 2006. (MoDC Poly # 9)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351532
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351532/suppl/GSM351532.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351532/suppl/GSM351532.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351534 | GPL570 |
|
16h_PolyRNA_serie2
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 23rd of November 2006. RNA extracted out of day5 MoDCs on the 4th of December 2006. (MoDC Poly # 9)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351534
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351534/suppl/GSM351534.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351534/suppl/GSM351534.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351535 | GPL570 |
|
16h_TotRNA_serie2
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 23rd of November 2006. RNA extracted out of day5 MoDCs on the 4th of December 2006. (MoDC Poly # 9)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351535
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351535/suppl/GSM351535.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351535/suppl/GSM351535.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351536 | GPL570 |
|
0h_PolyRNA_serie3
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 15th of December 2006. RNA extracted out of day5 MoDCs on the 9th of January 2007. (MoDC Poly # 10)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351536
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NO LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351536/suppl/GSM351536.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351536/suppl/GSM351536.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351537 | GPL570 |
|
0h_TotRNA_serie3
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 15th of December 2006. RNA extracted out of day5 MoDCs on the 9th of January 2007. (MoDC Poly # 10)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351537
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NO LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351537/suppl/GSM351537.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351537/suppl/GSM351537.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351538 | GPL570 |
|
4h_PolyRNA_serie3
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 15th of December 2006. RNA extracted out of day5 MoDCs on the 9th of January 2007. (MoDC Poly # 10)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351538
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351538/suppl/GSM351538.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351538/suppl/GSM351538.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351539 | GPL570 |
|
4h_TotRNA_serie3
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 15th of December 2006. RNA extracted out of day5 MoDCs on the 9th of January 2007. (MoDC Poly # 10)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351539
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351539/suppl/GSM351539.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351539/suppl/GSM351539.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351613 | GPL570 |
|
16h_PolyRNA_serie3
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 15th of December 2006. RNA extracted out of day5 MoDCs on the 9th of January 2007. (MoDC Poly # 10)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351613
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351613/suppl/GSM351613.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351613/suppl/GSM351613.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351615 | GPL570 |
|
16h_TotRNA_serie3
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 15th of December 2006. RNA extracted out of day5 MoDCs on the 9th of January 2007. (MoDC Poly # 10)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351615
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351615/suppl/GSM351615.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351615/suppl/GSM351615.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351616 | GPL570 |
|
0h_PolyRNA_serie4
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 12th of October 2006. RNA extracted out of day5 MoDCs on the 20th of October 2006. (MoDC Poly # 7)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351616
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NO LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351616/suppl/GSM351616.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351616/suppl/GSM351616.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351622 | GPL570 |
|
0h_TotRNA_serie4
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 12th of October 2006. RNA extracted out of day5 MoDCs on the 20th of October 2006. (MoDC Poly # 7)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351622
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NO LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351622/suppl/GSM351622.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351622/suppl/GSM351622.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351624 | GPL570 |
|
4h_PolyRNA_serie4
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 12th of October 2006. RNA extracted out of day5 MoDCs on the 20th of October 2006. (MoDC Poly # 7)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351624
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351624/suppl/GSM351624.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351624/suppl/GSM351624.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351638 | GPL570 |
|
4h_TotRNA_serie4
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 12th of October 2006. RNA extracted out of day5 MoDCs on the 20th of October 2006. (MoDC Poly # 7)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351638
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351638/suppl/GSM351638.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351638/suppl/GSM351638.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351640 | GPL570 |
|
16h_PolyRNA_serie4
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 12th of October 2006. RNA extracted out of day5 MoDCs on the 20th of October 2006. (MoDC Poly # 7)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351640
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351640/suppl/GSM351640.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351640/suppl/GSM351640.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
|
GSM351641 | GPL570 |
|
16h_TotRNA_serie4
|
monocyte-derived dendritic cells
|
Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 12th of October 2006. RNA extracted out of day5 MoDCs on the 20th of October 2006. (MoDC Poly # 7)
|
For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)
|
| Sample_geo_accession | GSM351641
| | Sample_status | Public on Dec 31 2009
| | Sample_submission_date | Dec 16 2008
| | Sample_last_update_date | Nov 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16h LPS
| | Sample_growth_protocol_ch1 | Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Standard Affymetrix labelling procedure
| | Sample_hyb_protocol | Standard Affymetrix hybridization procedure
| | Sample_scan_protocol | Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure
| | Sample_data_processing | The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Philippe,,Pierre
| | Sample_contact_email | pierre@ciml.univ-mrs.fr
| | Sample_contact_laboratory | Dendritic Cells - Philippe Pierre
| | Sample_contact_institute | CIML - CNRS - INSERM
| | Sample_contact_address | Campus Luminy - case 906
| | Sample_contact_city | Marseille
| | Sample_contact_zip/postal_code | 13288
| | Sample_contact_country | France
| | Sample_contact_web_link | www.ciml.univ-mrs.fr
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351641/suppl/GSM351641.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351641/suppl/GSM351641.CHP.gz
| | Sample_series_id | GSE14000
| | Sample_data_row_count | 54675
| | |
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