Result

Search results for the GEO ID: GSE23398

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GSM ID

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Title

Source name

Description

Characteristics

GSM573825

GPL1261

B6-CD4-LN-Biological replicate 1

FACS sorted CD4+ T cells

strain: C57BL/6 sex: male age: 3-week old tissue: pooled peripheral lymph nodes of two mice

Gene expression data from B6 mice

Sample_geo_accession	GSM573825
Sample_status	Public on Sep 18 2012
Sample_submission_date	Aug 03 2010
Sample_last_update_date	Sep 18 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three week old mice of various genotype were sacrificed and the peripheral lymph nodes were isolated. Axillary, brachial, inguinal, cervical and facial lymph nodes (LN) from sex- and age-matched B6, Sf, and Sf.Il2-/- mice were isolated, pooled, and single cell suspensions were prepared in PBS. CD4+ T cells were purified by depletion using biotinylated antibodies against B220, CD8, CD11b, CD11c and NK1.1 and magnetic beads (Miltenyi Biotec). The CD4-enriched cells were labeled with PE-anti-CD3 and Allophycocyanin (APC)-anti-CD4 antibodies and sorted at the UVA Flow Core facility by Fluorescence Assisted Cell Sorting (FACS) on a BD –Vantage cell sorter equipped with BD-Diva software. The purity of CD4+ T-cells was >99%.
Sample_growth_protocol_ch1	Three weeks old mice C57BL/6, Scurfy (Sf; B6.Cg-Foxp3sf/J) and Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) - termed as Sf.Il2-/-
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared using Rneasy miniprep kit (Qiagen) with on-column DNase digestion following manufacturer's protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to the standard target labeling protocols compatible with Affymetrix chips.
Sample_hyb_protocol	The samples were hybridized and stained per standard Affymetrix protocols at University of Virginia DNA sciences core facility. Mouse_430_2 arrays (Affymetrix, CA) were used for hybridization.
Sample_scan_protocol	The samples were scanned at Unversity of Virginia DNA sciences core using Affymetrix set-up.
Sample_data_processing	The data were The data were normalized using GC-RMA algorithm with software RMAExpress. Additionally analysis were performed using dChip, GCOS, R-statistical software equipped with LPE (Local Pooled Error) and SAM (Significance of Microarray) Bio-conductor packages.
Sample_platform_id	GPL1261
Sample_contact_name	Rahul,,Sharma
Sample_contact_email	rs3wn@virginia.edu
Sample_contact_department	Center for Immunity, Inflammation and Regenerative Medicine
Sample_contact_institute	University of Virginia
Sample_contact_address	Room 5768, Old Medical School Building, 21 Hospital Drive
Sample_contact_city	Charlottesville
Sample_contact_state	VA
Sample_contact_zip/postal_code	22908
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573825/suppl/GSM573825.CEL.gz
Sample_series_id	GSE23398
Sample_data_row_count	45037

GSM573826

GPL1261

Scurfy-CD4-LN-Biological replicate 1

FACS sorted CD4+ T cells

strain: Scurfy (Sf; B6.Cg-Foxp3sf/J) sex: male age: 3-week old tissue: peripheral lymph nodes

Gene expression data from Foxp3 mutant Scurfy (Sf) mice

Sample_geo_accession	GSM573826
Sample_status	Public on Sep 18 2012
Sample_submission_date	Aug 03 2010
Sample_last_update_date	Sep 18 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three week old mice of various genotype were sacrificed and the peripheral lymph nodes were isolated. Axillary, brachial, inguinal, cervical and facial lymph nodes (LN) from sex- and age-matched B6, Sf, and Sf.Il2-/- mice were isolated, pooled, and single cell suspensions were prepared in PBS. CD4+ T cells were purified by depletion using biotinylated antibodies against B220, CD8, CD11b, CD11c and NK1.1 and magnetic beads (Miltenyi Biotec). The CD4-enriched cells were labeled with PE-anti-CD3 and Allophycocyanin (APC)-anti-CD4 antibodies and sorted at the UVA Flow Core facility by Fluorescence Assisted Cell Sorting (FACS) on a BD –Vantage cell sorter equipped with BD-Diva software. The purity of CD4+ T-cells was >99%.
Sample_growth_protocol_ch1	Three weeks old mice C57BL/6, Scurfy (Sf; B6.Cg-Foxp3sf/J) and Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) - termed as Sf.Il2-/-
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared using Rneasy miniprep kit (Qiagen) with on-column DNase digestion following manufacturer's protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to the standard target labeling protocols compatible with Affymetrix chips.
Sample_hyb_protocol	The samples were hybridized and stained per standard Affymetrix protocols at University of Virginia DNA sciences core facility. Mouse_430_2 arrays (Affymetrix, CA) were used for hybridization.
Sample_scan_protocol	The samples were scanned at Unversity of Virginia DNA sciences core using Affymetrix set-up.
Sample_data_processing	The data were The data were normalized using GC-RMA algorithm with software RMAExpress. Additionally analysis were performed using dChip, GCOS, R-statistical software equipped with LPE (Local Pooled Error) and SAM (Significance of Microarray) Bio-conductor packages.
Sample_platform_id	GPL1261
Sample_contact_name	Rahul,,Sharma
Sample_contact_email	rs3wn@virginia.edu
Sample_contact_department	Center for Immunity, Inflammation and Regenerative Medicine
Sample_contact_institute	University of Virginia
Sample_contact_address	Room 5768, Old Medical School Building, 21 Hospital Drive
Sample_contact_city	Charlottesville
Sample_contact_state	VA
Sample_contact_zip/postal_code	22908
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573826/suppl/GSM573826.CEL.gz
Sample_series_id	GSE23398
Sample_data_row_count	45037

GSM573827

GPL1261

Scurfy-CD4-LN-Biological replicate 2

FACS sorted CD4+ T cells

strain: Scurfy (Sf; B6.Cg-Foxp3sf/J) sex: male age: 3-week old tissue: peripheral lymph nodes

Gene expression data from Foxp3 mutant Scurfy (Sf) mice

Sample_geo_accession	GSM573827
Sample_status	Public on Sep 18 2012
Sample_submission_date	Aug 03 2010
Sample_last_update_date	Sep 18 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three week old mice of various genotype were sacrificed and the peripheral lymph nodes were isolated. Axillary, brachial, inguinal, cervical and facial lymph nodes (LN) from sex- and age-matched B6, Sf, and Sf.Il2-/- mice were isolated, pooled, and single cell suspensions were prepared in PBS. CD4+ T cells were purified by depletion using biotinylated antibodies against B220, CD8, CD11b, CD11c and NK1.1 and magnetic beads (Miltenyi Biotec). The CD4-enriched cells were labeled with PE-anti-CD3 and Allophycocyanin (APC)-anti-CD4 antibodies and sorted at the UVA Flow Core facility by Fluorescence Assisted Cell Sorting (FACS) on a BD –Vantage cell sorter equipped with BD-Diva software. The purity of CD4+ T-cells was >99%.
Sample_growth_protocol_ch1	Three weeks old mice C57BL/6, Scurfy (Sf; B6.Cg-Foxp3sf/J) and Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) - termed as Sf.Il2-/-
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared using Rneasy miniprep kit (Qiagen) with on-column DNase digestion following manufacturer's protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to the standard target labeling protocols compatible with Affymetrix chips.
Sample_hyb_protocol	The samples were hybridized and stained per standard Affymetrix protocols at University of Virginia DNA sciences core facility. Mouse_430_2 arrays (Affymetrix, CA) were used for hybridization.
Sample_scan_protocol	The samples were scanned at Unversity of Virginia DNA sciences core using Affymetrix set-up.
Sample_data_processing	The data were The data were normalized using GC-RMA algorithm with software RMAExpress. Additionally analysis were performed using dChip, GCOS, R-statistical software equipped with LPE (Local Pooled Error) and SAM (Significance of Microarray) Bio-conductor packages.
Sample_platform_id	GPL1261
Sample_contact_name	Rahul,,Sharma
Sample_contact_email	rs3wn@virginia.edu
Sample_contact_department	Center for Immunity, Inflammation and Regenerative Medicine
Sample_contact_institute	University of Virginia
Sample_contact_address	Room 5768, Old Medical School Building, 21 Hospital Drive
Sample_contact_city	Charlottesville
Sample_contact_state	VA
Sample_contact_zip/postal_code	22908
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573827/suppl/GSM573827.CEL.gz
Sample_series_id	GSE23398
Sample_data_row_count	45037

GSM573828

GPL1261

Scurfy-CD4-LN-Biological replicate 3

FACS sorted CD4+ T cells

strain: Scurfy (Sf; B6.Cg-Foxp3sf/J) sex: male age: 3-week old tissue: peripheral lymph nodes

Gene expression data from Foxp3 mutant Scurfy (Sf) mice

Sample_geo_accession	GSM573828
Sample_status	Public on Sep 18 2012
Sample_submission_date	Aug 03 2010
Sample_last_update_date	Sep 18 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three week old mice of various genotype were sacrificed and the peripheral lymph nodes were isolated. Axillary, brachial, inguinal, cervical and facial lymph nodes (LN) from sex- and age-matched B6, Sf, and Sf.Il2-/- mice were isolated, pooled, and single cell suspensions were prepared in PBS. CD4+ T cells were purified by depletion using biotinylated antibodies against B220, CD8, CD11b, CD11c and NK1.1 and magnetic beads (Miltenyi Biotec). The CD4-enriched cells were labeled with PE-anti-CD3 and Allophycocyanin (APC)-anti-CD4 antibodies and sorted at the UVA Flow Core facility by Fluorescence Assisted Cell Sorting (FACS) on a BD –Vantage cell sorter equipped with BD-Diva software. The purity of CD4+ T-cells was >99%.
Sample_growth_protocol_ch1	Three weeks old mice C57BL/6, Scurfy (Sf; B6.Cg-Foxp3sf/J) and Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) - termed as Sf.Il2-/-
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared using Rneasy miniprep kit (Qiagen) with on-column DNase digestion following manufacturer's protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to the standard target labeling protocols compatible with Affymetrix chips.
Sample_hyb_protocol	The samples were hybridized and stained per standard Affymetrix protocols at University of Virginia DNA sciences core facility. Mouse_430_2 arrays (Affymetrix, CA) were used for hybridization.
Sample_scan_protocol	The samples were scanned at Unversity of Virginia DNA sciences core using Affymetrix set-up.
Sample_data_processing	The data were The data were normalized using GC-RMA algorithm with software RMAExpress. Additionally analysis were performed using dChip, GCOS, R-statistical software equipped with LPE (Local Pooled Error) and SAM (Significance of Microarray) Bio-conductor packages.
Sample_platform_id	GPL1261
Sample_contact_name	Rahul,,Sharma
Sample_contact_email	rs3wn@virginia.edu
Sample_contact_department	Center for Immunity, Inflammation and Regenerative Medicine
Sample_contact_institute	University of Virginia
Sample_contact_address	Room 5768, Old Medical School Building, 21 Hospital Drive
Sample_contact_city	Charlottesville
Sample_contact_state	VA
Sample_contact_zip/postal_code	22908
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573828/suppl/GSM573828.CEL.gz
Sample_series_id	GSE23398
Sample_data_row_count	45037

GSM573829

GPL1261

Sf.Il2-/--CD4-LN-Biological replicate 1

FACS sorted CD4+ T cells

strain: Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) [Sf.Il2-/-] sex: male age: 3-week old tissue: peripheral lymph nodes

Gene expression data from IL-2 deficienct Scurfy (Sf.Il2-/-) mice

Sample_geo_accession	GSM573829
Sample_status	Public on Sep 18 2012
Sample_submission_date	Aug 03 2010
Sample_last_update_date	Sep 18 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three week old mice of various genotype were sacrificed and the peripheral lymph nodes were isolated. Axillary, brachial, inguinal, cervical and facial lymph nodes (LN) from sex- and age-matched B6, Sf, and Sf.Il2-/- mice were isolated, pooled, and single cell suspensions were prepared in PBS. CD4+ T cells were purified by depletion using biotinylated antibodies against B220, CD8, CD11b, CD11c and NK1.1 and magnetic beads (Miltenyi Biotec). The CD4-enriched cells were labeled with PE-anti-CD3 and Allophycocyanin (APC)-anti-CD4 antibodies and sorted at the UVA Flow Core facility by Fluorescence Assisted Cell Sorting (FACS) on a BD –Vantage cell sorter equipped with BD-Diva software. The purity of CD4+ T-cells was >99%.
Sample_growth_protocol_ch1	Three weeks old mice C57BL/6, Scurfy (Sf; B6.Cg-Foxp3sf/J) and Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) - termed as Sf.Il2-/-
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared using Rneasy miniprep kit (Qiagen) with on-column DNase digestion following manufacturer's protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to the standard target labeling protocols compatible with Affymetrix chips.
Sample_hyb_protocol	The samples were hybridized and stained per standard Affymetrix protocols at University of Virginia DNA sciences core facility. Mouse_430_2 arrays (Affymetrix, CA) were used for hybridization.
Sample_scan_protocol	The samples were scanned at Unversity of Virginia DNA sciences core using Affymetrix set-up.
Sample_data_processing	The data were The data were normalized using GC-RMA algorithm with software RMAExpress. Additionally analysis were performed using dChip, GCOS, R-statistical software equipped with LPE (Local Pooled Error) and SAM (Significance of Microarray) Bio-conductor packages.
Sample_platform_id	GPL1261
Sample_contact_name	Rahul,,Sharma
Sample_contact_email	rs3wn@virginia.edu
Sample_contact_department	Center for Immunity, Inflammation and Regenerative Medicine
Sample_contact_institute	University of Virginia
Sample_contact_address	Room 5768, Old Medical School Building, 21 Hospital Drive
Sample_contact_city	Charlottesville
Sample_contact_state	VA
Sample_contact_zip/postal_code	22908
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573829/suppl/GSM573829.CEL.gz
Sample_series_id	GSE23398
Sample_data_row_count	45037

GSM573830

GPL1261

Sf.Il2-/--CD4-LN-Biological replicate 2

FACS sorted CD4+ T cells

strain: Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) [Sf.Il2-/-] sex: male age: 3-week old tissue: peripheral lymph nodes

Gene expression data from IL-2 deficienct Scurfy (Sf.Il2-/-) mice

Sample_geo_accession	GSM573830
Sample_status	Public on Sep 18 2012
Sample_submission_date	Aug 03 2010
Sample_last_update_date	Sep 18 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three week old mice of various genotype were sacrificed and the peripheral lymph nodes were isolated. Axillary, brachial, inguinal, cervical and facial lymph nodes (LN) from sex- and age-matched B6, Sf, and Sf.Il2-/- mice were isolated, pooled, and single cell suspensions were prepared in PBS. CD4+ T cells were purified by depletion using biotinylated antibodies against B220, CD8, CD11b, CD11c and NK1.1 and magnetic beads (Miltenyi Biotec). The CD4-enriched cells were labeled with PE-anti-CD3 and Allophycocyanin (APC)-anti-CD4 antibodies and sorted at the UVA Flow Core facility by Fluorescence Assisted Cell Sorting (FACS) on a BD –Vantage cell sorter equipped with BD-Diva software. The purity of CD4+ T-cells was >99%.
Sample_growth_protocol_ch1	Three weeks old mice C57BL/6, Scurfy (Sf; B6.Cg-Foxp3sf/J) and Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) - termed as Sf.Il2-/-
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared using Rneasy miniprep kit (Qiagen) with on-column DNase digestion following manufacturer's protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to the standard target labeling protocols compatible with Affymetrix chips.
Sample_hyb_protocol	The samples were hybridized and stained per standard Affymetrix protocols at University of Virginia DNA sciences core facility. Mouse_430_2 arrays (Affymetrix, CA) were used for hybridization.
Sample_scan_protocol	The samples were scanned at Unversity of Virginia DNA sciences core using Affymetrix set-up.
Sample_data_processing	The data were The data were normalized using GC-RMA algorithm with software RMAExpress. Additionally analysis were performed using dChip, GCOS, R-statistical software equipped with LPE (Local Pooled Error) and SAM (Significance of Microarray) Bio-conductor packages.
Sample_platform_id	GPL1261
Sample_contact_name	Rahul,,Sharma
Sample_contact_email	rs3wn@virginia.edu
Sample_contact_department	Center for Immunity, Inflammation and Regenerative Medicine
Sample_contact_institute	University of Virginia
Sample_contact_address	Room 5768, Old Medical School Building, 21 Hospital Drive
Sample_contact_city	Charlottesville
Sample_contact_state	VA
Sample_contact_zip/postal_code	22908
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573830/suppl/GSM573830.CEL.gz
Sample_series_id	GSE23398
Sample_data_row_count	45037

GSM573831

GPL1261

Sf.Il2-/--CD4-LN-Biological replicate 3

FACS sorted CD4+ T cells

strain: Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) [Sf.Il2-/-] sex: male age: 3-week old tissue: peripheral lymph nodes

Gene expression data from IL-2 deficienct Scurfy (Sf.Il2-/-) mice

Sample_geo_accession	GSM573831
Sample_status	Public on Sep 18 2012
Sample_submission_date	Aug 03 2010
Sample_last_update_date	Sep 18 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three week old mice of various genotype were sacrificed and the peripheral lymph nodes were isolated. Axillary, brachial, inguinal, cervical and facial lymph nodes (LN) from sex- and age-matched B6, Sf, and Sf.Il2-/- mice were isolated, pooled, and single cell suspensions were prepared in PBS. CD4+ T cells were purified by depletion using biotinylated antibodies against B220, CD8, CD11b, CD11c and NK1.1 and magnetic beads (Miltenyi Biotec). The CD4-enriched cells were labeled with PE-anti-CD3 and Allophycocyanin (APC)-anti-CD4 antibodies and sorted at the UVA Flow Core facility by Fluorescence Assisted Cell Sorting (FACS) on a BD –Vantage cell sorter equipped with BD-Diva software. The purity of CD4+ T-cells was >99%.
Sample_growth_protocol_ch1	Three weeks old mice C57BL/6, Scurfy (Sf; B6.Cg-Foxp3sf/J) and Scurfy mice with a null IL-2 gene (B6.129P2-Il2tm1Hor/J) - termed as Sf.Il2-/-
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared using Rneasy miniprep kit (Qiagen) with on-column DNase digestion following manufacturer's protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to the standard target labeling protocols compatible with Affymetrix chips.
Sample_hyb_protocol	The samples were hybridized and stained per standard Affymetrix protocols at University of Virginia DNA sciences core facility. Mouse_430_2 arrays (Affymetrix, CA) were used for hybridization.
Sample_scan_protocol	The samples were scanned at Unversity of Virginia DNA sciences core using Affymetrix set-up.
Sample_data_processing	The data were The data were normalized using GC-RMA algorithm with software RMAExpress. Additionally analysis were performed using dChip, GCOS, R-statistical software equipped with LPE (Local Pooled Error) and SAM (Significance of Microarray) Bio-conductor packages.
Sample_platform_id	GPL1261
Sample_contact_name	Rahul,,Sharma
Sample_contact_email	rs3wn@virginia.edu
Sample_contact_department	Center for Immunity, Inflammation and Regenerative Medicine
Sample_contact_institute	University of Virginia
Sample_contact_address	Room 5768, Old Medical School Building, 21 Hospital Drive
Sample_contact_city	Charlottesville
Sample_contact_state	VA
Sample_contact_zip/postal_code	22908
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM573nnn/GSM573831/suppl/GSM573831.CEL.gz
Sample_series_id	GSE23398
Sample_data_row_count	45037

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