Result

Search results for the GEO ID: GSE29241

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GSM ID

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Title

Source name

Description

Characteristics

GSM723040

GPL1261

Multipotent progenitor sample 1 (GM-MPP_1)

Multipotent progenitor (MPP) from mouse bone marrow obtained with stem cell cytokines plus GM-CSF

strain: C57BL/6 cell type: multipotent progenitor cell treatment: GM-CSF

BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

Sample_geo_accession	GSM723040
Sample_status	Public on Nov 13 2011
Sample_submission_date	May 12 2011
Sample_last_update_date	Nov 14 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
Sample_hyb_protocol	Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
Sample_scan_protocol	Arrays were scanned using Affymetrix GeneChip Scanner 3000.
Sample_data_processing	CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
Sample_platform_id	GPL1261
Sample_contact_name	Martin,,Zenke
Sample_contact_email	Martin.Zenke@rwth-aachen.de
Sample_contact_phone	+49-241-80 80760
Sample_contact_department	Cell Biology
Sample_contact_institute	Institute for Biomedical Engineering
Sample_contact_address	Universitatsklinikum Aachen, RWTH
Sample_contact_city	Aachen
Sample_contact_state	NRW
Sample_contact_zip/postal_code	52074
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723040/suppl/GSM723040_GM_MPP1.CEL.gz
Sample_series_id	GSE29241
Sample_data_row_count	45101

GSM723041

GPL1261

Multipotent progenitor sample 2 (GM-MPP_2)

Multipotent progenitor (MPP) from mouse bone marrow obtained with stem cell cytokines plus GM-CSF

strain: C57BL/6 cell type: multipotent progenitor cell treatment: GM-CSF

Sample_geo_accession	GSM723041
Sample_status	Public on Nov 13 2011
Sample_submission_date	May 12 2011
Sample_last_update_date	Nov 14 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
Sample_hyb_protocol	Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
Sample_scan_protocol	Arrays were scanned using Affymetrix GeneChip Scanner 3000.
Sample_data_processing	CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
Sample_platform_id	GPL1261
Sample_contact_name	Martin,,Zenke
Sample_contact_email	Martin.Zenke@rwth-aachen.de
Sample_contact_phone	+49-241-80 80760
Sample_contact_department	Cell Biology
Sample_contact_institute	Institute for Biomedical Engineering
Sample_contact_address	Universitatsklinikum Aachen, RWTH
Sample_contact_city	Aachen
Sample_contact_state	NRW
Sample_contact_zip/postal_code	52074
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723041/suppl/GSM723041_GM_MPP2.CEL.gz
Sample_series_id	GSE29241
Sample_data_row_count	45101

GSM723042

GPL1261

Dendritic cell sample 1 (GM-DC_1)

Dendritic cells obtained from GM-MPP with GM-CSF

cell type: dendritic cell treatment: GM-CSF strain: C57BL/6

Sample_geo_accession	GSM723042
Sample_status	Public on Nov 13 2011
Sample_submission_date	May 12 2011
Sample_last_update_date	Nov 14 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
Sample_hyb_protocol	Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
Sample_scan_protocol	Arrays were scanned using Affymetrix GeneChip Scanner 3000.
Sample_data_processing	CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
Sample_platform_id	GPL1261
Sample_contact_name	Martin,,Zenke
Sample_contact_email	Martin.Zenke@rwth-aachen.de
Sample_contact_phone	+49-241-80 80760
Sample_contact_department	Cell Biology
Sample_contact_institute	Institute for Biomedical Engineering
Sample_contact_address	Universitatsklinikum Aachen, RWTH
Sample_contact_city	Aachen
Sample_contact_state	NRW
Sample_contact_zip/postal_code	52074
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723042/suppl/GSM723042_GM_DC1.CEL.gz
Sample_series_id	GSE29241
Sample_data_row_count	45101

GSM723043

GPL1261

Dendritic cell sample 2 (GM-DC_2)

Dendritic cells obtained from GM-MPP with GM-CSF

strain: C57BL/6 cell type: dendritic cell treatment: GM-CSF

Sample_geo_accession	GSM723043
Sample_status	Public on Nov 13 2011
Sample_submission_date	May 12 2011
Sample_last_update_date	Nov 14 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
Sample_hyb_protocol	Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
Sample_scan_protocol	Arrays were scanned using Affymetrix GeneChip Scanner 3000.
Sample_data_processing	CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
Sample_platform_id	GPL1261
Sample_contact_name	Martin,,Zenke
Sample_contact_email	Martin.Zenke@rwth-aachen.de
Sample_contact_phone	+49-241-80 80760
Sample_contact_department	Cell Biology
Sample_contact_institute	Institute for Biomedical Engineering
Sample_contact_address	Universitatsklinikum Aachen, RWTH
Sample_contact_city	Aachen
Sample_contact_state	NRW
Sample_contact_zip/postal_code	52074
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723043/suppl/GSM723043_GM_DC2.CEL.gz
Sample_series_id	GSE29241
Sample_data_row_count	45101

GSM723044

GPL1261

Dendritic cell plus TNFa sample 1 (GM-TNFa-DC_1)

Dendritic cells obtained from GM-MPP with GM-CSF plus TNFa

strain: C57BL/6 cell type: dendritic cell treatment: GM-CSF and TNFa

Sample_geo_accession	GSM723044
Sample_status	Public on Nov 13 2011
Sample_submission_date	May 12 2011
Sample_last_update_date	Nov 14 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
Sample_hyb_protocol	Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
Sample_scan_protocol	Arrays were scanned using Affymetrix GeneChip Scanner 3000.
Sample_data_processing	CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
Sample_platform_id	GPL1261
Sample_contact_name	Martin,,Zenke
Sample_contact_email	Martin.Zenke@rwth-aachen.de
Sample_contact_phone	+49-241-80 80760
Sample_contact_department	Cell Biology
Sample_contact_institute	Institute for Biomedical Engineering
Sample_contact_address	Universitatsklinikum Aachen, RWTH
Sample_contact_city	Aachen
Sample_contact_state	NRW
Sample_contact_zip/postal_code	52074
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723044/suppl/GSM723044_GM_TNFa_DC1.CEL.gz
Sample_series_id	GSE29241
Sample_data_row_count	45101

GSM723045

GPL1261

Dendritic cell plus TNFa sample 2 (GM-TNFa-DC_2)

Dendritic cells obtained from GM-MPP with GM-CSF plus TNFa

strain: C57BL/6 cell type: dendritic cell treatment: GM-CSF and TNFa

Sample_geo_accession	GSM723045
Sample_status	Public on Nov 13 2011
Sample_submission_date	May 12 2011
Sample_last_update_date	Nov 14 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
Sample_hyb_protocol	Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
Sample_scan_protocol	Arrays were scanned using Affymetrix GeneChip Scanner 3000.
Sample_data_processing	CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
Sample_platform_id	GPL1261
Sample_contact_name	Martin,,Zenke
Sample_contact_email	Martin.Zenke@rwth-aachen.de
Sample_contact_phone	+49-241-80 80760
Sample_contact_department	Cell Biology
Sample_contact_institute	Institute for Biomedical Engineering
Sample_contact_address	Universitatsklinikum Aachen, RWTH
Sample_contact_city	Aachen
Sample_contact_state	NRW
Sample_contact_zip/postal_code	52074
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM723nnn/GSM723045/suppl/GSM723045_GM_TNFa_DC2.CEL.gz
Sample_series_id	GSE29241
Sample_data_row_count	45101

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