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Search results for the GEO ID: GSE35543

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Description

Characteristics

GSM870351

GPL1261

Mouse invivo nTreg cells, replicate pool 1

nTreg

strain: BALB/c genotype/variation: Rag1-deficient treatment: WT nTreg + WT iTreg cell type (sorted): nTreg

Gene expression interrogating 45101 transcripts nTreg 1 erica mouse 10-5-11_(Mouse430_2).CEL

Sample_geo_accession	GSM870351
Sample_status	Public on Dec 06 2012
Sample_submission_date	Feb 03 2012
Sample_last_update_date	Dec 06 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Pooled splenocytes and mesenteric lymph node cells were stained with anti-CD4-Pacific blue and sorted on the basis of antibody and EGFP fluorescence. Cultured iTreg cells were sorted on the basis of EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.96+/–0.14% and 84.31+/–0.68% respectively (n=120). For the treatment experiments, 1 ml of a cell suspension in PBS was injected into the peritoneal cavity of colitis mice that had lost 2.5+/– 5.7% of their initial body weight.
Sample_growth_protocol_ch1	Foxp3EGFP, Foxp3(delta)EGFP on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). BALB/c Rag1–/– mice and Il10–/– mice were obtained from the Jackson Laboratory. Il10–/– mice were crossed to Foxp3EGFP mice. The Animal Resource Committees at the Medical College of Wisconsin 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 all the iTregs, nTregs, and ex-iTreg experiments, two 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 Native (not activated) conventional CD4+T cells (GSE14415) as a common standard was identified and used for further analysis. The data was normalized using the RMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 2 independent arrays for each cell type and FDR<10% by the Rank Product package from Bioconductor.
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/GSM870nnn/GSM870351/suppl/GSM870351.CEL.gz
Sample_series_id	GSE35543
Sample_data_row_count	45101

GSM870352

GPL1261

Mouse invivo nTreg cells, replicate pool 2

nTreg

strain: BALB/c genotype/variation: Rag1-deficient treatment: WT nTreg + WT iTreg cell type (sorted): nTreg

Gene expression interrogating 45101 transcripts nTreg 2 erica mouse 10-5-11_(Mouse430_2).CEL

Sample_geo_accession	GSM870352
Sample_status	Public on Dec 06 2012
Sample_submission_date	Feb 03 2012
Sample_last_update_date	Dec 06 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Pooled splenocytes and mesenteric lymph node cells were stained with anti-CD4-Pacific blue and sorted on the basis of antibody and EGFP fluorescence. Cultured iTreg cells were sorted on the basis of EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.96+/–0.14% and 84.31+/–0.68% respectively (n=120). For the treatment experiments, 1 ml of a cell suspension in PBS was injected into the peritoneal cavity of colitis mice that had lost 2.5+/– 5.7% of their initial body weight.
Sample_growth_protocol_ch1	Foxp3EGFP, Foxp3(delta)EGFP on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). BALB/c Rag1–/– mice and Il10–/– mice were obtained from the Jackson Laboratory. Il10–/– mice were crossed to Foxp3EGFP mice. The Animal Resource Committees at the Medical College of Wisconsin 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 all the iTregs, nTregs, and ex-iTreg experiments, two 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 Native (not activated) conventional CD4+T cells (GSE14415) as a common standard was identified and used for further analysis. The data was normalized using the RMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 2 independent arrays for each cell type and FDR<10% by the Rank Product package from Bioconductor.
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/GSM870nnn/GSM870352/suppl/GSM870352.CEL.gz
Sample_series_id	GSE35543
Sample_data_row_count	45101

GSM870353

GPL1261

Mouse stable invitro iTreg cells, replicate pool 1

iTreg

strain: BALB/c genotype/variation: Rag1-deficient treatment: WT nTreg + WT iTreg cell type (sorted): iTreg

Gene expression interrogating 45101 transcripts iTreg 1 erica mouse 10-5-11_(Mouse430_2).CEL

Sample_geo_accession	GSM870353
Sample_status	Public on Dec 06 2012
Sample_submission_date	Feb 03 2012
Sample_last_update_date	Dec 06 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Pooled splenocytes and mesenteric lymph node cells were stained with anti-CD4-Pacific blue and sorted on the basis of antibody and EGFP fluorescence. Cultured iTreg cells were sorted on the basis of EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.96+/–0.14% and 84.31+/–0.68% respectively (n=120). For the treatment experiments, 1 ml of a cell suspension in PBS was injected into the peritoneal cavity of colitis mice that had lost 2.5+/– 5.7% of their initial body weight.
Sample_growth_protocol_ch1	Foxp3EGFP, Foxp3(delta)EGFP on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). BALB/c Rag1–/– mice and Il10–/– mice were obtained from the Jackson Laboratory. Il10–/– mice were crossed to Foxp3EGFP mice. The Animal Resource Committees at the Medical College of Wisconsin 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 all the iTregs, nTregs, and ex-iTreg experiments, two 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 Native (not activated) conventional CD4+T cells (GSE14415) as a common standard was identified and used for further analysis. The data was normalized using the RMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 2 independent arrays for each cell type and FDR<10% by the Rank Product package from Bioconductor.
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/GSM870nnn/GSM870353/suppl/GSM870353.CEL.gz
Sample_series_id	GSE35543
Sample_data_row_count	45101

GSM870354

GPL1261

Mouse stable invitro iTreg cells, replicate pool 2

iTreg

strain: BALB/c genotype/variation: Rag1-deficient treatment: WT nTreg + WT iTreg cell type (sorted): iTreg

Gene expression interrogating 45101 transcripts iTreg 2 erica mouse 10-5-11_(Mouse430_2).CEL

Sample_geo_accession	GSM870354
Sample_status	Public on Dec 06 2012
Sample_submission_date	Feb 03 2012
Sample_last_update_date	Dec 06 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Pooled splenocytes and mesenteric lymph node cells were stained with anti-CD4-Pacific blue and sorted on the basis of antibody and EGFP fluorescence. Cultured iTreg cells were sorted on the basis of EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.96+/–0.14% and 84.31+/–0.68% respectively (n=120). For the treatment experiments, 1 ml of a cell suspension in PBS was injected into the peritoneal cavity of colitis mice that had lost 2.5+/– 5.7% of their initial body weight.
Sample_growth_protocol_ch1	Foxp3EGFP, Foxp3(delta)EGFP on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). BALB/c Rag1–/– mice and Il10–/– mice were obtained from the Jackson Laboratory. Il10–/– mice were crossed to Foxp3EGFP mice. The Animal Resource Committees at the Medical College of Wisconsin 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 all the iTregs, nTregs, and ex-iTreg experiments, two 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 Native (not activated) conventional CD4+T cells (GSE14415) as a common standard was identified and used for further analysis. The data was normalized using the RMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 2 independent arrays for each cell type and FDR<10% by the Rank Product package from Bioconductor.
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/GSM870nnn/GSM870354/suppl/GSM870354.CEL.gz
Sample_series_id	GSE35543
Sample_data_row_count	45101

GSM870355

GPL1261

Mouse ex-iTreg cells, replicate pool 1

ex-iTreg

strain: BALB/c genotype/variation: Rag1-deficient treatment: WT nTreg + WT iTreg cell type (sorted): ex-iTreg

Gene expression interrogating 45101 transcripts exiTreg 1 erica mouse 10-5-11_(Mouse430_2).CEL

Sample_geo_accession	GSM870355
Sample_status	Public on Dec 06 2012
Sample_submission_date	Feb 03 2012
Sample_last_update_date	Dec 06 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Pooled splenocytes and mesenteric lymph node cells were stained with anti-CD4-Pacific blue and sorted on the basis of antibody and EGFP fluorescence. Cultured iTreg cells were sorted on the basis of EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.96+/–0.14% and 84.31+/–0.68% respectively (n=120). For the treatment experiments, 1 ml of a cell suspension in PBS was injected into the peritoneal cavity of colitis mice that had lost 2.5+/– 5.7% of their initial body weight.
Sample_growth_protocol_ch1	Foxp3EGFP, Foxp3(delta)EGFP on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). BALB/c Rag1–/– mice and Il10–/– mice were obtained from the Jackson Laboratory. Il10–/– mice were crossed to Foxp3EGFP mice. The Animal Resource Committees at the Medical College of Wisconsin 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 all the iTregs, nTregs, and ex-iTreg experiments, two 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 Native (not activated) conventional CD4+T cells (GSE14415) as a common standard was identified and used for further analysis. The data was normalized using the RMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 2 independent arrays for each cell type and FDR<10% by the Rank Product package from Bioconductor.
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/GSM870nnn/GSM870355/suppl/GSM870355.CEL.gz
Sample_series_id	GSE35543
Sample_data_row_count	45101

GSM870356

GPL1261

Mouse ex-iTreg cells, replicate pool 2

ex-iTreg

strain: BALB/c genotype/variation: Rag1-deficient treatment: WT nTreg + WT iTreg cell type (sorted): ex-iTreg

Gene expression interrogating 45101 transcripts exiTreg 2 erica mouse 10-5-11_(Mouse430_2).CEL

Sample_geo_accession	GSM870356
Sample_status	Public on Dec 06 2012
Sample_submission_date	Feb 03 2012
Sample_last_update_date	Dec 06 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Pooled splenocytes and mesenteric lymph node cells were stained with anti-CD4-Pacific blue and sorted on the basis of antibody and EGFP fluorescence. Cultured iTreg cells were sorted on the basis of EGFP fluorescence. All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.96+/–0.14% and 84.31+/–0.68% respectively (n=120). For the treatment experiments, 1 ml of a cell suspension in PBS was injected into the peritoneal cavity of colitis mice that had lost 2.5+/– 5.7% of their initial body weight.
Sample_growth_protocol_ch1	Foxp3EGFP, Foxp3(delta)EGFP on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). BALB/c Rag1–/– mice and Il10–/– mice were obtained from the Jackson Laboratory. Il10–/– mice were crossed to Foxp3EGFP mice. The Animal Resource Committees at the Medical College of Wisconsin 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 all the iTregs, nTregs, and ex-iTreg experiments, two 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 Native (not activated) conventional CD4+T cells (GSE14415) as a common standard was identified and used for further analysis. The data was normalized using the RMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 2 independent arrays for each cell type and FDR<10% by the Rank Product package from Bioconductor.
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/GSM870nnn/GSM870356/suppl/GSM870356.CEL.gz
Sample_series_id	GSE35543
Sample_data_row_count	45101

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