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Search results for the GEO ID: GSE19512

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Description

Characteristics

GSM486563

GPL1261

Mouse in vivo nTreg cells, replicate pool 1

EGFP+ Thy1.1+ nTreg cells sorted from the spleens and lymph nodes of treated mice, replicate pool 1

source: FoxP3-deficient BALB/c Foxp3K276X mice age: 50 days old cell type: nTreg

Gene expression interrogating 45101 transcripts

Sample_geo_accession	GSM486563
Sample_status	Public on Jun 30 2011
Sample_submission_date	Dec 16 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Pooled splenocytes and lymph node cells were stained with either anti-CD4-PE, or anti-CD4-Pacific blue and anti-CD45RB-APC as appropriate, and sorted on the basis of antibody and EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.8+0.2% and 87.6+1.6% respectively (n=23). For the Foxp3-deficient rescue experiments, 200 microliters of a cell suspension in PBS was injected into the peritoneal cavity of pups within the first 30 hours following birth.
Sample_growth_protocol_ch1	Foxp3EGFP, Foxp3(delta)EGFP, and Foxp3K276X mice on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). C57BL/6 Rag1-/- mice were obtained from the Jackson Laboratory and backcrossed to BALB/c mice for over 20 generations. Rescued Foxp3K276X/ K276X females and Foxp3 K276X males were mated to generate litters where all progeny were Foxp3-deficient. The Animal Resource Committees at the Medical College of Wisconsin and at the University of California, Los Angeles approved all animal experiments and moribund mice were sacrificed and analyzed per these protocols.
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	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000.
Sample_data_processing	For both iTregs and nTreg experiments, three sets of arrays were performed, and the results were averaged. The subset of probe sets whose expression increased or decreased by twofold or more relative to Tconv cells as a common standard was identified and used for further analysis. The data was normalized using the justRMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 3 independent arrays for each cell type and scored P < 0.05 by the rank product test.
Sample_platform_id	GPL1261
Sample_contact_name	Martin,,Hessner
Sample_contact_email	mhessner@mcw.edu
Sample_contact_phone	414-456-4496
Sample_contact_fax	414-456-6663
Sample_contact_laboratory	Max McGee National Research Center for Juvenile Diabetes
Sample_contact_department	Pediatrics
Sample_contact_institute	Medical College of Wisconsin
Sample_contact_address	8701 Watertown Plank Road
Sample_contact_city	Milwaukee
Sample_contact_state	WI
Sample_contact_zip/postal_code	53226
Sample_contact_country	USA
Sample_contact_web_link	http://www.mcw.edu/MaxMcGeeResearchCenter.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486563/suppl/GSM486563_nTreg_invivo_rep1.CEL.gz
Sample_series_id	GSE19512
Sample_data_row_count	45101

GSM486564

GPL1261

Mouse in vivo nTreg cells, replicate pool 2

EGFP+ Thy1.1+ nTreg cells sorted from the spleens and lymph nodes of treated mice, replicate pool 2

source: FoxP3-deficient BALB/c Foxp3K276X mice age: 50 days old cell type: nTreg

Gene expression interrogating 45101 transcripts

Sample_geo_accession	GSM486564
Sample_status	Public on Jun 30 2011
Sample_submission_date	Dec 16 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Pooled splenocytes and lymph node cells were stained with either anti-CD4-PE, or anti-CD4-Pacific blue and anti-CD45RB-APC as appropriate, and sorted on the basis of antibody and EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.8+0.2% and 87.6+1.6% respectively (n=23). For the Foxp3-deficient rescue experiments, 200 microliters of a cell suspension in PBS was injected into the peritoneal cavity of pups within the first 30 hours following birth.
Sample_growth_protocol_ch1	Foxp3EGFP, Foxp3(delta)EGFP, and Foxp3K276X mice on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). C57BL/6 Rag1-/- mice were obtained from the Jackson Laboratory and backcrossed to BALB/c mice for over 20 generations. Rescued Foxp3K276X/ K276X females and Foxp3 K276X males were mated to generate litters where all progeny were Foxp3-deficient. The Animal Resource Committees at the Medical College of Wisconsin and at the University of California, Los Angeles approved all animal experiments and moribund mice were sacrificed and analyzed per these protocols.
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	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000.
Sample_data_processing	For both iTregs and nTreg experiments, three sets of arrays were performed, and the results were averaged. The subset of probe sets whose expression increased or decreased by twofold or more relative to Tconv cells as a common standard was identified and used for further analysis. The data was normalized using the justRMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 3 independent arrays for each cell type and scored P < 0.05 by the rank product test.
Sample_platform_id	GPL1261
Sample_contact_name	Martin,,Hessner
Sample_contact_email	mhessner@mcw.edu
Sample_contact_phone	414-456-4496
Sample_contact_fax	414-456-6663
Sample_contact_laboratory	Max McGee National Research Center for Juvenile Diabetes
Sample_contact_department	Pediatrics
Sample_contact_institute	Medical College of Wisconsin
Sample_contact_address	8701 Watertown Plank Road
Sample_contact_city	Milwaukee
Sample_contact_state	WI
Sample_contact_zip/postal_code	53226
Sample_contact_country	USA
Sample_contact_web_link	http://www.mcw.edu/MaxMcGeeResearchCenter.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486564/suppl/GSM486564_nTreg_invivo_rep2.CEL.gz
Sample_series_id	GSE19512
Sample_data_row_count	45101

GSM486565

GPL1261

Mouse in vivo nTreg cells, replicate pool 3

EGFP+ Thy1.1+ nTreg cells sorted from the spleens and lymph nodes of treated mice, replicate pool 3

source: FoxP3-deficient BALB/c Foxp3K276X mice age: 50 days old cell type: nTreg

Gene expression interrogating 45101 transcripts

Sample_geo_accession	GSM486565
Sample_status	Public on Jun 30 2011
Sample_submission_date	Dec 16 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Pooled splenocytes and lymph node cells were stained with either anti-CD4-PE, or anti-CD4-Pacific blue and anti-CD45RB-APC as appropriate, and sorted on the basis of antibody and EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.8+0.2% and 87.6+1.6% respectively (n=23). For the Foxp3-deficient rescue experiments, 200 microliters of a cell suspension in PBS was injected into the peritoneal cavity of pups within the first 30 hours following birth.
Sample_growth_protocol_ch1	Foxp3EGFP, Foxp3(delta)EGFP, and Foxp3K276X mice on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). C57BL/6 Rag1-/- mice were obtained from the Jackson Laboratory and backcrossed to BALB/c mice for over 20 generations. Rescued Foxp3K276X/ K276X females and Foxp3 K276X males were mated to generate litters where all progeny were Foxp3-deficient. The Animal Resource Committees at the Medical College of Wisconsin and at the University of California, Los Angeles approved all animal experiments and moribund mice were sacrificed and analyzed per these protocols.
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	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000.
Sample_data_processing	For both iTregs and nTreg experiments, three sets of arrays were performed, and the results were averaged. The subset of probe sets whose expression increased or decreased by twofold or more relative to Tconv cells as a common standard was identified and used for further analysis. The data was normalized using the justRMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 3 independent arrays for each cell type and scored P < 0.05 by the rank product test.
Sample_platform_id	GPL1261
Sample_contact_name	Martin,,Hessner
Sample_contact_email	mhessner@mcw.edu
Sample_contact_phone	414-456-4496
Sample_contact_fax	414-456-6663
Sample_contact_laboratory	Max McGee National Research Center for Juvenile Diabetes
Sample_contact_department	Pediatrics
Sample_contact_institute	Medical College of Wisconsin
Sample_contact_address	8701 Watertown Plank Road
Sample_contact_city	Milwaukee
Sample_contact_state	WI
Sample_contact_zip/postal_code	53226
Sample_contact_country	USA
Sample_contact_web_link	http://www.mcw.edu/MaxMcGeeResearchCenter.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486565/suppl/GSM486565_nTreg_invivo_rep3.CEL.gz
Sample_series_id	GSE19512
Sample_data_row_count	45101

GSM486566

GPL1261

Mouse in vivo iTreg cells, replicate pool 1

EGFP+ Thy1.1+ iTreg cells sorted from the spleens and lymph nodes of treated mice, replicate pool 1

source: FoxP3-deficient BALB/c Foxp3K276X mice age: 50 days old cell type: iTreg

Gene expression interrogating 45101 transcripts

Sample_geo_accession	GSM486566
Sample_status	Public on Jun 30 2011
Sample_submission_date	Dec 16 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Pooled splenocytes and lymph node cells were stained with either anti-CD4-PE, or anti-CD4-Pacific blue and anti-CD45RB-APC as appropriate, and sorted on the basis of antibody and EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.8+0.2% and 87.6+1.6% respectively (n=23). For the Foxp3-deficient rescue experiments, 200 microliters of a cell suspension in PBS was injected into the peritoneal cavity of pups within the first 30 hours following birth.
Sample_growth_protocol_ch1	Foxp3EGFP, Foxp3(delta)EGFP, and Foxp3K276X mice on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). C57BL/6 Rag1-/- mice were obtained from the Jackson Laboratory and backcrossed to BALB/c mice for over 20 generations. Rescued Foxp3K276X/ K276X females and Foxp3 K276X males were mated to generate litters where all progeny were Foxp3-deficient. The Animal Resource Committees at the Medical College of Wisconsin and at the University of California, Los Angeles approved all animal experiments and moribund mice were sacrificed and analyzed per these protocols.
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	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000.
Sample_data_processing	For both iTregs and nTreg experiments, three sets of arrays were performed, and the results were averaged. The subset of probe sets whose expression increased or decreased by twofold or more relative to Tconv cells as a common standard was identified and used for further analysis. The data was normalized using the justRMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 3 independent arrays for each cell type and scored P < 0.05 by the rank product test.
Sample_platform_id	GPL1261
Sample_contact_name	Martin,,Hessner
Sample_contact_email	mhessner@mcw.edu
Sample_contact_phone	414-456-4496
Sample_contact_fax	414-456-6663
Sample_contact_laboratory	Max McGee National Research Center for Juvenile Diabetes
Sample_contact_department	Pediatrics
Sample_contact_institute	Medical College of Wisconsin
Sample_contact_address	8701 Watertown Plank Road
Sample_contact_city	Milwaukee
Sample_contact_state	WI
Sample_contact_zip/postal_code	53226
Sample_contact_country	USA
Sample_contact_web_link	http://www.mcw.edu/MaxMcGeeResearchCenter.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486566/suppl/GSM486566_iTreg_invivo_rep1.CEL.gz
Sample_series_id	GSE19512
Sample_data_row_count	45101

GSM486567

GPL1261

Mouse in vivo iTreg cells, replicate pool 2

EGFP+ Thy1.1+ iTreg cells sorted from the spleens and lymph nodes of treated mice, replicate pool 2

source: FoxP3-deficient BALB/c Foxp3K276X mice age: 50 days old cell type: iTreg

Gene expression interrogating 45101 transcripts

Sample_geo_accession	GSM486567
Sample_status	Public on Jun 30 2011
Sample_submission_date	Dec 16 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Pooled splenocytes and lymph node cells were stained with either anti-CD4-PE, or anti-CD4-Pacific blue and anti-CD45RB-APC as appropriate, and sorted on the basis of antibody and EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.8+0.2% and 87.6+1.6% respectively (n=23). For the Foxp3-deficient rescue experiments, 200 microliters of a cell suspension in PBS was injected into the peritoneal cavity of pups within the first 30 hours following birth.
Sample_growth_protocol_ch1	Foxp3EGFP, Foxp3(delta)EGFP, and Foxp3K276X mice on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). C57BL/6 Rag1-/- mice were obtained from the Jackson Laboratory and backcrossed to BALB/c mice for over 20 generations. Rescued Foxp3K276X/ K276X females and Foxp3 K276X males were mated to generate litters where all progeny were Foxp3-deficient. The Animal Resource Committees at the Medical College of Wisconsin and at the University of California, Los Angeles approved all animal experiments and moribund mice were sacrificed and analyzed per these protocols.
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	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000.
Sample_data_processing	For both iTregs and nTreg experiments, three sets of arrays were performed, and the results were averaged. The subset of probe sets whose expression increased or decreased by twofold or more relative to Tconv cells as a common standard was identified and used for further analysis. The data was normalized using the justRMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 3 independent arrays for each cell type and scored P < 0.05 by the rank product test.
Sample_platform_id	GPL1261
Sample_contact_name	Martin,,Hessner
Sample_contact_email	mhessner@mcw.edu
Sample_contact_phone	414-456-4496
Sample_contact_fax	414-456-6663
Sample_contact_laboratory	Max McGee National Research Center for Juvenile Diabetes
Sample_contact_department	Pediatrics
Sample_contact_institute	Medical College of Wisconsin
Sample_contact_address	8701 Watertown Plank Road
Sample_contact_city	Milwaukee
Sample_contact_state	WI
Sample_contact_zip/postal_code	53226
Sample_contact_country	USA
Sample_contact_web_link	http://www.mcw.edu/MaxMcGeeResearchCenter.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486567/suppl/GSM486567_iTreg_invivo_rep2.CEL.gz
Sample_series_id	GSE19512
Sample_data_row_count	45101

GSM486568

GPL1261

Mouse in vivo iTreg cells, replicate pool 3

EGFP+ Thy1.1+ iTreg cells sorted from the spleens and lymph nodes of treated mice, replicate pool 3

source: FoxP3-deficient BALB/c Foxp3K276X mice age: 50 days old cell type: iTreg

Gene expression interrogating 45101 transcripts

Sample_geo_accession	GSM486568
Sample_status	Public on Jun 30 2011
Sample_submission_date	Dec 16 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Pooled splenocytes and lymph node cells were stained with either anti-CD4-PE, or anti-CD4-Pacific blue and anti-CD45RB-APC as appropriate, and sorted on the basis of antibody and EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.8+0.2% and 87.6+1.6% respectively (n=23). For the Foxp3-deficient rescue experiments, 200 microliters of a cell suspension in PBS was injected into the peritoneal cavity of pups within the first 30 hours following birth.
Sample_growth_protocol_ch1	Foxp3EGFP, Foxp3(delta)EGFP, and Foxp3K276X mice on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). C57BL/6 Rag1-/- mice were obtained from the Jackson Laboratory and backcrossed to BALB/c mice for over 20 generations. Rescued Foxp3K276X/ K276X females and Foxp3 K276X males were mated to generate litters where all progeny were Foxp3-deficient. The Animal Resource Committees at the Medical College of Wisconsin and at the University of California, Los Angeles approved all animal experiments and moribund mice were sacrificed and analyzed per these protocols.
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	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000.
Sample_data_processing	For both iTregs and nTreg experiments, three sets of arrays were performed, and the results were averaged. The subset of probe sets whose expression increased or decreased by twofold or more relative to Tconv cells as a common standard was identified and used for further analysis. The data was normalized using the justRMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 3 independent arrays for each cell type and scored P < 0.05 by the rank product test.
Sample_platform_id	GPL1261
Sample_contact_name	Martin,,Hessner
Sample_contact_email	mhessner@mcw.edu
Sample_contact_phone	414-456-4496
Sample_contact_fax	414-456-6663
Sample_contact_laboratory	Max McGee National Research Center for Juvenile Diabetes
Sample_contact_department	Pediatrics
Sample_contact_institute	Medical College of Wisconsin
Sample_contact_address	8701 Watertown Plank Road
Sample_contact_city	Milwaukee
Sample_contact_state	WI
Sample_contact_zip/postal_code	53226
Sample_contact_country	USA
Sample_contact_web_link	http://www.mcw.edu/MaxMcGeeResearchCenter.htm
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486568/suppl/GSM486568_iTreg_invivo_rep3.CEL.gz
Sample_series_id	GSE19512
Sample_data_row_count	45101

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