Search results for the GEO ID: GSE28408  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM702185 | GPL1261 |
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T_SHG001-Mouse430_2_2, Ly6G+DC1
|
bone marrow, Ly6G+ DC
|
strain: C57BL/6
tissue: bone marrow
cell type: CD11c+/MHC II+/Ly6G+ dendritic cells
|
T_SHG001-Mouse430_2_2
Gene expression data of sorted Ly6G+DC from BM cultures.
|
| Sample_geo_accession | GSM702185
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Apr 05 2011
| | Sample_last_update_date | Feb 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Crude bone marrow cells were propagated from C57BL/6 mice. The cells were cultured at 37C in the presence of 10 ng/ml GM-CSF to generate CD11c+ DC populations. On day 6, CD11c+/MHC II+/Ly6G+ DC and CD11c+/MHC II+/Ly6G- DC were simultaneously sorted from the same cultures by FACSAria.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to standard RT-IVT methods. First- and-second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays, which detect approximately 44,000 mouse transcripts representing over 34,000 well-characterized mouse genes (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommended procedures. The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
| | Sample_scan_protocol | The fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix).
| | Sample_data_processing | The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant mean target intensity (TGT) of 250.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hironori,,Matsushima
| | Sample_contact_email | hironori.matsushima@utoledo.edu
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of Toledo College of Medicine
| | Sample_contact_address | 3000 Arlington Avenue Mail Stop 1021
| | Sample_contact_city | Toledo
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43614
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM702nnn/GSM702185/suppl/GSM702185.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM702nnn/GSM702185/suppl/GSM702185.CHP.gz
| | Sample_series_id | GSE28408
| | Sample_data_row_count | 45101
| | |
|
GSM702186 | GPL1261 |
|
T_SHG002-Mouse430_2_2, Ly6G-DC1
|
bone marrow, Ly6G- DC
|
strain: C57BL/6
tissue: bone marrow
cell type: CD11c+/MHC II+/Ly6G- dendritic cells
|
T_SHG002-Mouse430_2_2
Gene expression data of sorted Ly6G-DC from BM cultures.
|
| Sample_geo_accession | GSM702186
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Apr 05 2011
| | Sample_last_update_date | Feb 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Crude bone marrow cells were propagated from C57BL/6 mice. The cells were cultured at 37C in the presence of 10 ng/ml GM-CSF to generate CD11c+ DC populations. On day 6, CD11c+/MHC II+/Ly6G+ DC and CD11c+/MHC II+/Ly6G- DC were simultaneously sorted from the same cultures by FACSAria.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to standard RT-IVT methods. First- and-second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays, which detect approximately 44,000 mouse transcripts representing over 34,000 well-characterized mouse genes (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommended procedures. The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
| | Sample_scan_protocol | The fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix).
| | Sample_data_processing | The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant mean target intensity (TGT) of 250.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hironori,,Matsushima
| | Sample_contact_email | hironori.matsushima@utoledo.edu
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of Toledo College of Medicine
| | Sample_contact_address | 3000 Arlington Avenue Mail Stop 1021
| | Sample_contact_city | Toledo
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43614
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM702nnn/GSM702186/suppl/GSM702186.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM702nnn/GSM702186/suppl/GSM702186.CHP.gz
| | Sample_series_id | GSE28408
| | Sample_data_row_count | 45101
| | |
|
GSM702187 | GPL1261 |
|
T_SHG003-Mouse430_2, Ly6G+DC2
|
bone marrow, Ly6G+ DC
|
strain: C57BL/6
tissue: bone marrow
cell type: CD11c+/MHC II+/Ly6G+ dendritic cells
|
T_SHG003-Mouse430_2
Gene expression data of sorted Ly6G+DC from BM cultures.
|
| Sample_geo_accession | GSM702187
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Apr 05 2011
| | Sample_last_update_date | Feb 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Crude bone marrow cells were propagated from C57BL/6 mice. The cells were cultured at 37C in the presence of 10 ng/ml GM-CSF to generate CD11c+ DC populations. On day 6, CD11c+/MHC II+/Ly6G+ DC and CD11c+/MHC II+/Ly6G- DC were simultaneously sorted from the same cultures by FACSAria.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to standard RT-IVT methods. First- and-second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays, which detect approximately 44,000 mouse transcripts representing over 34,000 well-characterized mouse genes (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommended procedures. The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
| | Sample_scan_protocol | The fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix).
| | Sample_data_processing | The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant mean target intensity (TGT) of 250.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hironori,,Matsushima
| | Sample_contact_email | hironori.matsushima@utoledo.edu
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of Toledo College of Medicine
| | Sample_contact_address | 3000 Arlington Avenue Mail Stop 1021
| | Sample_contact_city | Toledo
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43614
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM702nnn/GSM702187/suppl/GSM702187.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM702nnn/GSM702187/suppl/GSM702187.CHP.gz
| | Sample_series_id | GSE28408
| | Sample_data_row_count | 45101
| | |
|
GSM702188 | GPL1261 |
|
T_SHG004-Mouse430_2, Ly6G-DC2
|
bone marrow, Ly6G- DC
|
strain: C57BL/6
tissue: bone marrow
cell type: CD11c+/MHC II+/Ly6G- dendritic cells
|
T_SHG004-Mouse430_2
Gene expression data of sorted Ly6G-DC from BM cultures.
|
| Sample_geo_accession | GSM702188
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Apr 05 2011
| | Sample_last_update_date | Feb 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Crude bone marrow cells were propagated from C57BL/6 mice. The cells were cultured at 37C in the presence of 10 ng/ml GM-CSF to generate CD11c+ DC populations. On day 6, CD11c+/MHC II+/Ly6G+ DC and CD11c+/MHC II+/Ly6G- DC were simultaneously sorted from the same cultures by FACSAria.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to standard RT-IVT methods. First- and-second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays, which detect approximately 44,000 mouse transcripts representing over 34,000 well-characterized mouse genes (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommended procedures. The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
| | Sample_scan_protocol | The fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix).
| | Sample_data_processing | The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant mean target intensity (TGT) of 250.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hironori,,Matsushima
| | Sample_contact_email | hironori.matsushima@utoledo.edu
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of Toledo College of Medicine
| | Sample_contact_address | 3000 Arlington Avenue Mail Stop 1021
| | Sample_contact_city | Toledo
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43614
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM702nnn/GSM702188/suppl/GSM702188.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM702nnn/GSM702188/suppl/GSM702188.CHP.gz
| | Sample_series_id | GSE28408
| | Sample_data_row_count | 45101
| | |
|
GSM702189 | GPL1261 |
|
T_SHG007-Mouse430_2, Ly6G+DC3
|
bone marrow, Ly6G+ DC
|
strain: C57BL/6
tissue: bone marrow
cell type: CD11c+/MHC II+/Ly6G+ dendritic cells
|
T_SHG007-Mouse430_2
Gene expression data of sorted Ly6G+DC from BM cultures.
|
| Sample_geo_accession | GSM702189
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Apr 05 2011
| | Sample_last_update_date | Feb 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Crude bone marrow cells were propagated from C57BL/6 mice. The cells were cultured at 37C in the presence of 10 ng/ml GM-CSF to generate CD11c+ DC populations. On day 6, CD11c+/MHC II+/Ly6G+ DC and CD11c+/MHC II+/Ly6G- DC were simultaneously sorted from the same cultures by FACSAria.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to standard RT-IVT methods. First- and-second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays, which detect approximately 44,000 mouse transcripts representing over 34,000 well-characterized mouse genes (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommended procedures. The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
| | Sample_scan_protocol | The fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix).
| | Sample_data_processing | The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant mean target intensity (TGT) of 250.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hironori,,Matsushima
| | Sample_contact_email | hironori.matsushima@utoledo.edu
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of Toledo College of Medicine
| | Sample_contact_address | 3000 Arlington Avenue Mail Stop 1021
| | Sample_contact_city | Toledo
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43614
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM702nnn/GSM702189/suppl/GSM702189.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM702nnn/GSM702189/suppl/GSM702189.CHP.gz
| | Sample_series_id | GSE28408
| | Sample_data_row_count | 45101
| | |
|
GSM702190 | GPL1261 |
|
T_SHG006-Mouse430_2, Ly6G-DC3
|
bone marrow, Ly6G- DC
|
strain: C57BL/6
tissue: bone marrow
cell type: CD11c+/MHC II+/Ly6G- dendritic cells
|
T_SHG006-Mouse430_2
Gene expression data of sorted Ly6G-DC from BM cultures.
|
| Sample_geo_accession | GSM702190
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Apr 05 2011
| | Sample_last_update_date | Feb 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Crude bone marrow cells were propagated from C57BL/6 mice. The cells were cultured at 37C in the presence of 10 ng/ml GM-CSF to generate CD11c+ DC populations. On day 6, CD11c+/MHC II+/Ly6G+ DC and CD11c+/MHC II+/Ly6G- DC were simultaneously sorted from the same cultures by FACSAria.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was processed and labeled according to standard RT-IVT methods. First- and-second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays, which detect approximately 44,000 mouse transcripts representing over 34,000 well-characterized mouse genes (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommended procedures. The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
| | Sample_scan_protocol | The fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix).
| | Sample_data_processing | The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant mean target intensity (TGT) of 250.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Hironori,,Matsushima
| | Sample_contact_email | hironori.matsushima@utoledo.edu
| | Sample_contact_department | Medical Microbiology and Immunology
| | Sample_contact_institute | University of Toledo College of Medicine
| | Sample_contact_address | 3000 Arlington Avenue Mail Stop 1021
| | Sample_contact_city | Toledo
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43614
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM702nnn/GSM702190/suppl/GSM702190.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM702nnn/GSM702190/suppl/GSM702190.CHP.gz
| | Sample_series_id | GSE28408
| | Sample_data_row_count | 45101
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