Result

Search results for the GEO ID: GSE16644

(Click on the check boxes provided under "Select for analysis", to initiate grouping)

(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM417691

GPL1261

BMDCs-uninfected-24hr-sorted-rep1

Bone marrow-derived dendritic cells, uninfected controls, 24h sorted

strain: BALB/c gender: Female age: 8 weeks origin: bone marrow cells culture: 14 days in vitro with GM-CSF

Leishmania_1_DC_expr_1NS24.txt

Sample_geo_accession	GSM417691
Sample_status	Public on Jun 15 2010
Sample_submission_date	Jun 16 2009
Sample_last_update_date	Jun 18 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	On day 14, DCs were infected or not with L. amazonensis amastigotes at parasite/DC ratios of 4/1. The samples were gently pipetted to dissociate DC clusters and to promote contact between microorganisms and DCs. Infected cells and uninfected cells (controls run in parallel) were then placed at 34°C for 24 hours. After staining with the PE-Cy5 stained M5/114 mAb, DCs were sorted using the BD FACSDiva software (BD Biosciences). The sorter was equipped with 405, 488 and 633 nm laser excitation wavelengths. PE-Cy5 and DsRed2 fluorescences were collected through 695/40 and 576/26 bandpass filters respectively. Forward and side laser scatter were displayed on a linear scale, and used to discard cell debris. To avoid the sorting of cell doublets or cell aggregates, single cells were sequentially selected on SSC-H/SSC-W and FSC-H/FSC-W dot plots. Infected DCs were sorted by selecting cells expressing both MHC Class II molecules and DsRed2 (M5/114 PE-Cy5/DsRed2 dot plot).
Sample_growth_protocol_ch1	On day 0, bone marrow cells were seeded at 2x106 cells per 100 mm-diameter bacteriological grade Petri dish (Falcon, Becton Dickinson Labware) in 10 ml of Iscove’s modified Dulbecco’s medium (IMDM; BioWhittaker Europe) supplemented with 10% heat-inactivated fetal calf serum (FCS; Dutscher), 1.5% supernatant from a J558 cell line producing murine GM-CSF (Zal et al., 1994), 50 U/ml penicillin, 50 µg/ml streptomycin, 50 µM 2-mercaptoethanol and 2 mM glutamine (complete IMDM). Cultures were incubated at 37°C in a humidified atmosphere with 7% CO2. On day 3, 10 ml of complete IMDM was added. On day 6, suspended cells and loosely adherent cells were harvested using prewarmed 1% EDTA in Dulbecco’s PBS without Ca2+ and Mg2+ (Biochrom AG). Recovered cells were further cultured in the same conditions as above, except that complete IMDM was supplemented with 10% of the primary culture supernatant. On day 10, cells were harvested with EDTA as above, and distributed in hydrophobic 6-well plates (Greiner) at a concentration of 9x105 cells/well in 3 ml complete IMDM. On day 13, 2 ml of medium was removed from each well and replaced by 2 ml of fresh medium.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from biological replicates using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s instructions. Evaluation of RNA quality was performed by optical density measurement and by electrophoresis on a Lab-on-a-chip product using the Agilent 2100 Bioanalyzer (Agilent). RNA was quantified using Nanodrop (Kisker).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Affymetrix two-cycle labeling protocol
Sample_hyb_protocol	GeneChip hybridizations were performed according to the Affymetrix protocol.
Sample_scan_protocol	GeneChipScanner (GSC) 3000 was used with GeneChip Operating Software (GCOS).
Sample_data_processing	QC assessment of Affymetrix recommended QC metrics was done using the AffyGCQC program[Osorio-y-Fortéa et al., 2008]. Data processing, background correction, normalization and signal quantification were carried out using the GC-Robust Multiarray Analysis (GC-RMA) algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Eric,,Prina
Sample_contact_email	eric.prina@pasteur.fr
Sample_contact_phone	+33 (0)140613514
Sample_contact_fax	+33 (0)140613332
Sample_contact_laboratory	IPPIC
Sample_contact_department	Parasitology and Mycology
Sample_contact_institute	Institut Pasteur
Sample_contact_address	25 rue du Dr Roux
Sample_contact_city	Paris
Sample_contact_zip/postal_code	75724
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417691/suppl/GSM417691.CEL.gz
Sample_series_id	GSE16644
Sample_data_row_count	45101

GSM417719

GPL1261

BMDCs-uninfected-24hr-sorted-rep2

Bone marrow-derived dendritic cells, uninfected controls, 24h sorted

strain: BALB/c gender: Female age: 8 weeks origin: bone marrow cells culture: 14 days in vitro with GM-CSF

Leishmania_2_DC_expr_2NS24.txt

Sample_geo_accession	GSM417719
Sample_status	Public on Jun 15 2010
Sample_submission_date	Jun 16 2009
Sample_last_update_date	Jun 18 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	On day 14, DCs were infected or not with L. amazonensis amastigotes at parasite/DC ratios of 4/1. The samples were gently pipetted to dissociate DC clusters and to promote contact between microorganisms and DCs. Infected cells and uninfected cells (controls run in parallel) were then placed at 34°C for 24 hours. After staining with the PE-Cy5 stained M5/114 mAb, DCs were sorted using the BD FACSDiva software (BD Biosciences). The sorter was equipped with 405, 488 and 633 nm laser excitation wavelengths. PE-Cy5 and DsRed2 fluorescences were collected through 695/40 and 576/26 bandpass filters respectively. Forward and side laser scatter were displayed on a linear scale, and used to discard cell debris. To avoid the sorting of cell doublets or cell aggregates, single cells were sequentially selected on SSC-H/SSC-W and FSC-H/FSC-W dot plots. Infected DCs were sorted by selecting cells expressing both MHC Class II molecules and DsRed2 (M5/114 PE-Cy5/DsRed2 dot plot).
Sample_growth_protocol_ch1	On day 0, bone marrow cells were seeded at 2x106 cells per 100 mm-diameter bacteriological grade Petri dish (Falcon, Becton Dickinson Labware) in 10 ml of Iscove’s modified Dulbecco’s medium (IMDM; BioWhittaker Europe) supplemented with 10% heat-inactivated fetal calf serum (FCS; Dutscher), 1.5% supernatant from a J558 cell line producing murine GM-CSF (Zal et al., 1994), 50 U/ml penicillin, 50 µg/ml streptomycin, 50 µM 2-mercaptoethanol and 2 mM glutamine (complete IMDM). Cultures were incubated at 37°C in a humidified atmosphere with 7% CO2. On day 3, 10 ml of complete IMDM was added. On day 6, suspended cells and loosely adherent cells were harvested using prewarmed 1% EDTA in Dulbecco’s PBS without Ca2+ and Mg2+ (Biochrom AG). Recovered cells were further cultured in the same conditions as above, except that complete IMDM was supplemented with 10% of the primary culture supernatant. On day 10, cells were harvested with EDTA as above, and distributed in hydrophobic 6-well plates (Greiner) at a concentration of 9x105 cells/well in 3 ml complete IMDM. On day 13, 2 ml of medium was removed from each well and replaced by 2 ml of fresh medium.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from biological replicates using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s instructions. Evaluation of RNA quality was performed by optical density measurement and by electrophoresis on a Lab-on-a-chip product using the Agilent 2100 Bioanalyzer (Agilent). RNA was quantified using Nanodrop (Kisker).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Affymetrix two-cycle labeling protocol
Sample_hyb_protocol	GeneChip hybridizations were performed according to the Affymetrix protocol.
Sample_scan_protocol	GeneChipScanner (GSC) 3000 was used with GeneChip Operating Software (GCOS).
Sample_data_processing	QC assessment of Affymetrix recommended QC metrics was done using the AffyGCQC program[Osorio-y-Fortéa et al., 2008]. Data processing, background correction, normalization and signal quantification were carried out using the GC-Robust Multiarray Analysis (GC-RMA) algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Eric,,Prina
Sample_contact_email	eric.prina@pasteur.fr
Sample_contact_phone	+33 (0)140613514
Sample_contact_fax	+33 (0)140613332
Sample_contact_laboratory	IPPIC
Sample_contact_department	Parasitology and Mycology
Sample_contact_institute	Institut Pasteur
Sample_contact_address	25 rue du Dr Roux
Sample_contact_city	Paris
Sample_contact_zip/postal_code	75724
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417719/suppl/GSM417719.CEL.gz
Sample_series_id	GSE16644
Sample_data_row_count	45101

GSM417721

GPL1261

BMDCs-uninfected-24hr-sorted-rep3

Bone marrow-derived dendritic cells, uninfected controls, 24h sorted

strain: BALB/c gender: Female age: 8 weeks origin: bone marrow cells culture: 14 days in vitro with GM-CSF

Leishmania_DC_expr_3NS24.txt

Sample_geo_accession	GSM417721
Sample_status	Public on Jun 15 2010
Sample_submission_date	Jun 16 2009
Sample_last_update_date	Jun 18 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	On day 14, DCs were infected or not with L. amazonensis amastigotes at parasite/DC ratios of 4/1. The samples were gently pipetted to dissociate DC clusters and to promote contact between microorganisms and DCs. Infected cells and uninfected cells (controls run in parallel) were then placed at 34°C for 24 hours. After staining with the PE-Cy5 stained M5/114 mAb, DCs were sorted using the BD FACSDiva software (BD Biosciences). The sorter was equipped with 405, 488 and 633 nm laser excitation wavelengths. PE-Cy5 and DsRed2 fluorescences were collected through 695/40 and 576/26 bandpass filters respectively. Forward and side laser scatter were displayed on a linear scale, and used to discard cell debris. To avoid the sorting of cell doublets or cell aggregates, single cells were sequentially selected on SSC-H/SSC-W and FSC-H/FSC-W dot plots. Infected DCs were sorted by selecting cells expressing both MHC Class II molecules and DsRed2 (M5/114 PE-Cy5/DsRed2 dot plot).
Sample_growth_protocol_ch1	On day 0, bone marrow cells were seeded at 2x106 cells per 100 mm-diameter bacteriological grade Petri dish (Falcon, Becton Dickinson Labware) in 10 ml of Iscove’s modified Dulbecco’s medium (IMDM; BioWhittaker Europe) supplemented with 10% heat-inactivated fetal calf serum (FCS; Dutscher), 1.5% supernatant from a J558 cell line producing murine GM-CSF (Zal et al., 1994), 50 U/ml penicillin, 50 µg/ml streptomycin, 50 µM 2-mercaptoethanol and 2 mM glutamine (complete IMDM). Cultures were incubated at 37°C in a humidified atmosphere with 7% CO2. On day 3, 10 ml of complete IMDM was added. On day 6, suspended cells and loosely adherent cells were harvested using prewarmed 1% EDTA in Dulbecco’s PBS without Ca2+ and Mg2+ (Biochrom AG). Recovered cells were further cultured in the same conditions as above, except that complete IMDM was supplemented with 10% of the primary culture supernatant. On day 10, cells were harvested with EDTA as above, and distributed in hydrophobic 6-well plates (Greiner) at a concentration of 9x105 cells/well in 3 ml complete IMDM. On day 13, 2 ml of medium was removed from each well and replaced by 2 ml of fresh medium.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from biological replicates using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s instructions. Evaluation of RNA quality was performed by optical density measurement and by electrophoresis on a Lab-on-a-chip product using the Agilent 2100 Bioanalyzer (Agilent). RNA was quantified using Nanodrop (Kisker).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Affymetrix two-cycle labeling protocol
Sample_hyb_protocol	GeneChip hybridizations were performed according to the Affymetrix protocol.
Sample_scan_protocol	GeneChipScanner (GSC) 3000 was used with GeneChip Operating Software (GCOS).
Sample_data_processing	QC assessment of Affymetrix recommended QC metrics was done using the AffyGCQC program[Osorio-y-Fortéa et al., 2008]. Data processing, background correction, normalization and signal quantification were carried out using the GC-Robust Multiarray Analysis (GC-RMA) algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Eric,,Prina
Sample_contact_email	eric.prina@pasteur.fr
Sample_contact_phone	+33 (0)140613514
Sample_contact_fax	+33 (0)140613332
Sample_contact_laboratory	IPPIC
Sample_contact_department	Parasitology and Mycology
Sample_contact_institute	Institut Pasteur
Sample_contact_address	25 rue du Dr Roux
Sample_contact_city	Paris
Sample_contact_zip/postal_code	75724
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417721/suppl/GSM417721.CEL.gz
Sample_series_id	GSE16644
Sample_data_row_count	45101

GSM417722

GPL1261

BMDCs-infected-24hr-sorted-rep1

Bone marrow-derived dendritic cells, infected aLV79, 24h sorted

strain: BALB/c gender: Female age: 8 weeks origin: bone marrow cells culture: 14 days in vitro with GM-CSF infection: aLV79 for 24 hours

Leishmania_DC_expr_1a24.txt

Sample_geo_accession	GSM417722
Sample_status	Public on Jun 15 2010
Sample_submission_date	Jun 16 2009
Sample_last_update_date	Jun 18 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	On day 14, DCs were infected or not with L. amazonensis amastigotes at parasite/DC ratios of 4/1. The samples were gently pipetted to dissociate DC clusters and to promote contact between microorganisms and DCs. Infected cells and uninfected cells (controls run in parallel) were then placed at 34°C for 24 hours. After staining with the PE-Cy5 stained M5/114 mAb, DCs were sorted using the BD FACSDiva software (BD Biosciences). The sorter was equipped with 405, 488 and 633 nm laser excitation wavelengths. PE-Cy5 and DsRed2 fluorescences were collected through 695/40 and 576/26 bandpass filters respectively. Forward and side laser scatter were displayed on a linear scale, and used to discard cell debris. To avoid the sorting of cell doublets or cell aggregates, single cells were sequentially selected on SSC-H/SSC-W and FSC-H/FSC-W dot plots. Infected DCs were sorted by selecting cells expressing both MHC Class II molecules and DsRed2 (M5/114 PE-Cy5/DsRed2 dot plot).
Sample_growth_protocol_ch1	On day 0, bone marrow cells were seeded at 2x106 cells per 100 mm-diameter bacteriological grade Petri dish (Falcon, Becton Dickinson Labware) in 10 ml of Iscove’s modified Dulbecco’s medium (IMDM; BioWhittaker Europe) supplemented with 10% heat-inactivated fetal calf serum (FCS; Dutscher), 1.5% supernatant from a J558 cell line producing murine GM-CSF (Zal et al., 1994), 50 U/ml penicillin, 50 µg/ml streptomycin, 50 µM 2-mercaptoethanol and 2 mM glutamine (complete IMDM). Cultures were incubated at 37°C in a humidified atmosphere with 7% CO2. On day 3, 10 ml of complete IMDM was added. On day 6, suspended cells and loosely adherent cells were harvested using prewarmed 1% EDTA in Dulbecco’s PBS without Ca2+ and Mg2+ (Biochrom AG). Recovered cells were further cultured in the same conditions as above, except that complete IMDM was supplemented with 10% of the primary culture supernatant. On day 10, cells were harvested with EDTA as above, and distributed in hydrophobic 6-well plates (Greiner) at a concentration of 9x105 cells/well in 3 ml complete IMDM. On day 13, 2 ml of medium was removed from each well and replaced by 2 ml of fresh medium.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from biological replicates using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s instructions. Evaluation of RNA quality was performed by optical density measurement and by electrophoresis on a Lab-on-a-chip product using the Agilent 2100 Bioanalyzer (Agilent). RNA was quantified using Nanodrop (Kisker).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Affymetrix two-cycle labeling protocol
Sample_hyb_protocol	GeneChip hybridizations were performed according to the Affymetrix protocol.
Sample_scan_protocol	GeneChipScanner (GSC) 3000 was used with GeneChip Operating Software (GCOS).
Sample_data_processing	QC assessment of Affymetrix recommended QC metrics was done using the AffyGCQC program[Osorio-y-Fortéa et al., 2008]. Data processing, background correction, normalization and signal quantification were carried out using the GC-Robust Multiarray Analysis (GC-RMA) algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Eric,,Prina
Sample_contact_email	eric.prina@pasteur.fr
Sample_contact_phone	+33 (0)140613514
Sample_contact_fax	+33 (0)140613332
Sample_contact_laboratory	IPPIC
Sample_contact_department	Parasitology and Mycology
Sample_contact_institute	Institut Pasteur
Sample_contact_address	25 rue du Dr Roux
Sample_contact_city	Paris
Sample_contact_zip/postal_code	75724
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417722/suppl/GSM417722.CEL.gz
Sample_series_id	GSE16644
Sample_data_row_count	45101

GSM417724

GPL1261

BMDCs-infected-24hr-sorted-rep2

Bone marrow-derived dendritic cells, infected aLV79, 24h sorted

strain: BALB/c gender: Female age: 8 weeks origin: bone marrow cells culture: 14 days in vitro with GM-CSF infection: aLV79 for 24 hours

Leishmania_DC_expr_2a24.txt

Sample_geo_accession	GSM417724
Sample_status	Public on Jun 15 2010
Sample_submission_date	Jun 16 2009
Sample_last_update_date	Jun 18 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	On day 14, DCs were infected or not with L. amazonensis amastigotes at parasite/DC ratios of 4/1. The samples were gently pipetted to dissociate DC clusters and to promote contact between microorganisms and DCs. Infected cells and uninfected cells (controls run in parallel) were then placed at 34°C for 24 hours. After staining with the PE-Cy5 stained M5/114 mAb, DCs were sorted using the BD FACSDiva software (BD Biosciences). The sorter was equipped with 405, 488 and 633 nm laser excitation wavelengths. PE-Cy5 and DsRed2 fluorescences were collected through 695/40 and 576/26 bandpass filters respectively. Forward and side laser scatter were displayed on a linear scale, and used to discard cell debris. To avoid the sorting of cell doublets or cell aggregates, single cells were sequentially selected on SSC-H/SSC-W and FSC-H/FSC-W dot plots. Infected DCs were sorted by selecting cells expressing both MHC Class II molecules and DsRed2 (M5/114 PE-Cy5/DsRed2 dot plot).
Sample_growth_protocol_ch1	On day 0, bone marrow cells were seeded at 2x106 cells per 100 mm-diameter bacteriological grade Petri dish (Falcon, Becton Dickinson Labware) in 10 ml of Iscove’s modified Dulbecco’s medium (IMDM; BioWhittaker Europe) supplemented with 10% heat-inactivated fetal calf serum (FCS; Dutscher), 1.5% supernatant from a J558 cell line producing murine GM-CSF (Zal et al., 1994), 50 U/ml penicillin, 50 µg/ml streptomycin, 50 µM 2-mercaptoethanol and 2 mM glutamine (complete IMDM). Cultures were incubated at 37°C in a humidified atmosphere with 7% CO2. On day 3, 10 ml of complete IMDM was added. On day 6, suspended cells and loosely adherent cells were harvested using prewarmed 1% EDTA in Dulbecco’s PBS without Ca2+ and Mg2+ (Biochrom AG). Recovered cells were further cultured in the same conditions as above, except that complete IMDM was supplemented with 10% of the primary culture supernatant. On day 10, cells were harvested with EDTA as above, and distributed in hydrophobic 6-well plates (Greiner) at a concentration of 9x105 cells/well in 3 ml complete IMDM. On day 13, 2 ml of medium was removed from each well and replaced by 2 ml of fresh medium.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from biological replicates using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s instructions. Evaluation of RNA quality was performed by optical density measurement and by electrophoresis on a Lab-on-a-chip product using the Agilent 2100 Bioanalyzer (Agilent). RNA was quantified using Nanodrop (Kisker).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Affymetrix two-cycle labeling protocol
Sample_hyb_protocol	GeneChip hybridizations were performed according to the Affymetrix protocol.
Sample_scan_protocol	GeneChipScanner (GSC) 3000 was used with GeneChip Operating Software (GCOS).
Sample_data_processing	QC assessment of Affymetrix recommended QC metrics was done using the AffyGCQC program[Osorio-y-Fortéa et al., 2008]. Data processing, background correction, normalization and signal quantification were carried out using the GC-Robust Multiarray Analysis (GC-RMA) algorithm.
Sample_platform_id	GPL1261
Sample_contact_name	Eric,,Prina
Sample_contact_email	eric.prina@pasteur.fr
Sample_contact_phone	+33 (0)140613514
Sample_contact_fax	+33 (0)140613332
Sample_contact_laboratory	IPPIC
Sample_contact_department	Parasitology and Mycology
Sample_contact_institute	Institut Pasteur
Sample_contact_address	25 rue du Dr Roux
Sample_contact_city	Paris
Sample_contact_zip/postal_code	75724
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417724/suppl/GSM417724.CEL.gz
Sample_series_id	GSE16644
Sample_data_row_count	45101

Make groups for comparisons

(2 groups will be compared at a time)

Select GSMs and click on "Add groups"

Enter the group name here:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes