title: NKT.4+.Sp#2

description: NKT.4+.Sp#2, CD4+ iNKT cells from Spleen


title: NKT.44+NK1.1-.Th#1

status: Public on Apr 29 2010

type: RNA

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

country: USA

institute: Harvard Medical School

description: NKT.44+NK1.1-.Th#1, Developing thymic iNKT cells, stage 2

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: thymus

label_protocol: Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

extract_protocol: Homogenize, stain  MACS enrichment, Double sort (FACS Aria)

tag: age

value: 6 weeks

tag: exclusion markers

value: CD8a Ter119 CD19 CD11c CD11b Ly6/Gr-1 CD8a PI NK1.1

tag: genetic background

tag: phenotype markers

value: aGC CD1d tet CD3 CD44

tag: separation method

value: dissection/trimming

tag: Sex

value: male


title: NK.MCMV7.Sp#2

description: NK.MCMV7.Sp#2, Splenic NK cells MCMV d7 PI

source_name: spleen

extract_protocol: Glass slide teasing,  FACS sorting

value: CD3 CD4 CD5 CD8 CD19 Gr-1 Ter119


title: NKT.4-.Sp#2

description: NKT.4-.Sp#2, CD4- iNKT cells from Spleen

extract_protocol: homogenize, ACK lyse, stain  MACS enrichment, double sort (FACS Aria)

value: PI CD19 B220 CD11b Ter119 CD4

value: TCRbeta+ aGalCer tet+ CD4-


title: NK.MCMV7.Sp#1

description: NK.MCMV7.Sp#1, Splenic NK cells MCMV d7 PI


title: NK.H+.MCMV7.Sp#1

description: NK.H+.MCMV7.Sp#1, Splenic Ly49H+ NK cells from B6 mice 7 days following MCMV infection

value: NK1.1+ TCRb- Ly49H+


title: NK.H+.MCMV1.Sp#3

description: NK.H+.MCMV1.Sp#3, Splenic Ly49H+ NK cells from B6 mice 1.5 days following MCMV infection


title: NK.H+.MCMV1.Sp#2

description: NK.H+.MCMV1.Sp#2, Splenic Ly49H+ NK cells from B6 mice 1.5 days following MCMV infection


title: NK.H+.MCMV1.Sp#1

description: NK.H+.MCMV1.Sp#1, Splenic Ly49H+ NK cells from B6 mice 1.5 days following MCMV infection


title: NK.DAP12-.Sp#2

description: NK.DAP12-.Sp#2, Splenic NK cells from DAP12-/- mice


title: NK.DAP12-.Sp#3

description: NK.DAP12-.Sp#3, Splenic NK cells from DAP12-/- mice


title: NK.DAP12-.Sp#1

description: NK.DAP12-.Sp#1, Splenic NK cells from DAP12-/- mice


title: NKT.4+.Sp#1

description: NKT.4+.Sp#1, CD4+ iNKT cells from Spleen

extract_protocol: homogenize, ACK lysis, stain  MACS enrichement + double sort on FACS Aria

value: CD19 B220 Ter119 Cd11b PI

value: TCRb aGalCer-loaded CD1d tetramer CD4


title: NKT.4+.Lv#3

description: NKT.4+.Lv#3, CD4+ iNKT cells from Liver

source_name: liver

extract_protocol: homogenize, ficoll, stain  double sort on FACS Aria

value: PI B220

value: CD45 TCRb aGalCer-loaded CD1d tet CD4


title: NK.b2m-.Sp#3

description: NK.b2m-.Sp#3, Splenic NK cells from B2m-/- mice

value: NK1.1+ TCRb-


title: NK.MCMV7.Sp#3

description: NK.MCMV7.Sp#3, Splenic NK cells MCMV d7 PI


title: NK.b2m-.Sp#2

description: NK.b2m-.Sp#2, Splenic NK cells from B2m-/- mice


title: NK.DAP10-.Sp#3

description: NK.DAP10-.Sp#3, Splenic NK cells from DAP10-/- mice

value: 7 weeks


title: NK.DAP10-.Sp#1

description: NK.DAP10-.Sp#1, Splenic NK cells from DAP10-/- mice


title: NK.49CI-.Sp#2

description: NK.49CI-.Sp#2, Splenic NK cells, Ly49CI- subset

extract_protocol: Glass slide teasing


title: NK.b2m-.Sp#1

description: NK.b2m-.Sp#1, Splenic NK cells from B2m-/- mice


title: NK.49CI+.Sp#3

description: NK.49CI+.Sp#3, Splenic NK cells, Ly49CI+ subset


title: NK.49CI+.Sp#1

description: NK.49CI+.Sp#1, Splenic NK cells, Ly49CI+ subset


title: DC.IIhilang-103-11blo.SLN#2

description: DC.IIhilang-103-11blo.SLN#2, skin draining LN MHC IIhi langerin- CD103- CD11b- dendritic cell

source_name: iliac, axilary and inguinal lymph nodes

extract_protocol: 15 minutes digestion with Liberase Blenzyme 3

value: 10 weeks

value: CD4 CD8

value: MHCIIhi CD11c+ Langerin- CD103- CD11b-


title: DC.IIhilang-103-11blo.SLN#1

description: DC.IIhilang-103-11blo.SLN#1, skin draining LN MHC IIhi langerin- CD103- CD11b- dendritic cell


title: DC.IIhilang-103-11b+.SLN#2

description: DC.IIhilang-103-11b+.SLN#2, skin draining LN MHC IIhi langerin- CD103- CD11b+ dendritic cell

value: MHCIIhi CD11c+ Langerin- CD103- CD11b+


title: DC.IIhilang-103-11b+.SLN#3

description: DC.IIhilang-103-11b+.SLN#3, skin draining LN MHC IIhi langerin- CD103- CD11b+ dendritic cell


title: NK.49CI-.Sp#3

description: NK.49CI-.Sp#3, Splenic NK cells, Ly49CI- subset

value: 6 weeks


title: DC.IIhilang-103-11b+.SLN#1

description: DC.IIhilang-103-11b+.SLN#1, skin draining LN MHC IIhi langerin- CD103- CD11b+ dendritic cell

value: dissection/trimming


title: DC.IIhilang+103-11b+.SLN#3

description: DC.IIhilang+103-11b+.SLN#3, skin draining LN MHC IIhi langerin+  CD103- CD11b+ dendritic cell

value: MHCIIhi CD11c+ Langerin+ CD103- CD11b+

value: male


title: DC.IIhilang+103-11b+.SLN#1

description: DC.IIhilang+103-11b+.SLN#1, skin draining LN MHC IIhi langerin+  CD103- CD11b+ dendritic cell


title: DC.IIhilang-103-11blo.SLN#3

description: DC.IIhilang-103-11blo.SLN#3, skin draining LN MHC IIhi langerin- CD103- CD11b- dendritic cell


title: DC.IIhilang+103+11blo.SLN#3

description: DC.IIhilang+103+11blo.SLN#3, skin draining LN MHC IIhi langerin+ CD103+ CD11blo dendritic cell

value: MHCIIhi CD11c+ Langerin+ CD103+ CD11b-


title: DC.IIhilang+103-11b+.SLN#2

description: DC.IIhilang+103-11b+.SLN#2, skin draining LN MHC IIhi langerin+  CD103- CD11b+ dendritic cell


title: DC.IIhilang+103+11blo.SLN#2

description: DC.IIhilang+103+11blo.SLN#2, skin draining LN MHC IIhi langerin+ CD103+ CD11blo dendritic cell


title: DC.8-4-11b+.Sp#3

description: DC.8-4-11b+.Sp#3, spleen double negative dendritic cell

extract_protocol: Liberase Blendzymes III, DNAse I digestion  CD3e, CD19, GR1, NK1.1 MACS depletion

value: PI SA-PECy7

value: CD11b CD11c CD45 CD8a CD4


title: NK.DAP10-.Sp#2

description: NK.DAP10-.Sp#2, Splenic NK cells from DAP10-/- mice

value: CD3 CD4 CD5 CD8 CD19 Gr-1 Ter119


title: DC.8-4-11b+.Sp#1

description: DC.8-4-11b+.Sp#1, spleen double negative dendritic cell

extract_protocol: collagenase, dispase, DNAse digestion  CD3e, CD19, GR1, NK1.1 MACS depletion

value: CD11b CD4 CD45 CD11c CD8a


title: DC.8-4-11b+.Sp#2

description: DC.8-4-11b+.Sp#2, spleen double negative dendritic cell

extract_protocol: Liberase Blendzymes III, DNAse I digestion  CD3, CD19, GR1, NK1.1 MACS depletion


title: NK.49CI-.Sp#1

description: NK.49CI-.Sp#1, Splenic NK cells, Ly49CI- subset


title: DC.8-4-11b+.MLN#4

description: DC.8-4-11b+.MLN#4, mesenteric LN double negative dendritic cell

source_name: Mesenteric LN

extract_protocol: digestion using Liberase III + DNase I  CD3, CD19, GR1, NK1.1, Ter-119 using MACS beads

value: CD45-APC CD11b-FITC CD11c-eFluor780 CD4-PE CD8a-eFluor450


title: DC.8-4-11b+.MLN#5

description: DC.8-4-11b+.MLN#5, mesenteric LN double negative dendritic cell


title: NK.49CI+.Sp#2

description: NK.49CI+.Sp#2, Splenic NK cells, Ly49CI+ subset


title: DC.8-4-11b+.MLN#3

description: DC.8-4-11b+.MLN#3, mesenteric LN double negative dendritic cell

extract_protocol: Blendzyme liberase III + DNase digestion  CD3, CD19, NK1.1, GR1, Ter119 MACS depletion

value: CD11b-FITC CD4-PE CD11c-Alexa750 CD8a-PacificBlue CD45-APC


title: DC.8+.SLN#1

description: DC.8+.SLN#1, skin draining LN CD8+ dendritic cell

source_name: Subcutaneous LNs

extract_protocol: Blendzyme liberase III + DNase digestion  CD3, CD19, NK1.1, GR1, MACS depletion


title: DC.8+.SLN#2

description: DC.8+.SLN#2, skin draining LN CD8+ dendritic cell

extract_protocol: Blendzyme liberase III + DNase digestion  CD3, CD19 MACS depletion


title: DC.8+.SLN#3

description: DC.8+.SLN#3, skin draining LN CD8+ dendritic cell


title: DC.4+.SLN#1

description: DC.4+.SLN#1, skin draining LN CD4+dendritic cell


title: DC.4+.SLN#3

description: DC.4+.SLN#3, skin draining LN CD4+dendritic cell


title: DC.4+.SLN#2

description: DC.4+.SLN#2, skin draining LN CD4+dendritic cell

extract_protocol: Blendzyme liberase III + DNase digestionCD3,  CD3, CD19, NK1.1, GR1 MACS depletion


title: DC.4+.MLN#2

description: DC.4+.MLN#2, mesenteric LN CD4+ dendritic cell


title: DC.4+.MLN#3

description: DC.4+.MLN#3, mesenteric LN CD4+ dendritic cell


title: DC.4+.MLN#1

description: DC.4+.MLN#1, mesenteric LN CD4+ dendritic cell

extract_protocol: Blendzyme liberase III + DNase digestion  CD3, CD19, NK1.1, GR1  MACS depletion


title: DC.8+.MLN#2

description: DC.8+.MLN#2, mesenteric LN CD8+ dendritic cell

extract_protocol: Blendzyme liberase III + DNase digestion  CD3, CD19, GR1, NK1.1, Ter119 MACS depletion


title: DC.103+11b-.Lv#2

description: DC.103+11b-.Lv#2, liver CD103+ dendritic cells

extract_protocol: Disruption using syringe, ACK lysis

value: 8 weeks

value: CD45+ CD11c+ MHC-II+ CD11b low CD103+


title: DC.IIhilang+103+11blo.SLN#1

description: DC.IIhilang+103+11blo.SLN#1, skin draining LN MHC IIhi langerin+ CD103+ CD11blo dendritic cell

value: 10 weeks


title: DC.8+.MLN#3

description: DC.8+.MLN#3, mesenteric LN CD8+ dendritic cell


title: DC.103+11b-.Lv#1

description: DC.103+11b-.Lv#1, liver CD103+ dendritic cells


title: DC.103+11b-.Lu#2

description: DC.103+11b-.Lu#2, lung CD103+ dendritic cells

source_name: lung

value: Positive CD11c selection

value: CD11chi CD11b low CD103+ MHCII+ SiglecF-


title: DC.103+11b-.Lu#1

description: DC.103+11b-.Lu#1, lung CD103+ dendritic cells


title: DC.103+11b-.Lu#3

description: DC.103+11b-.Lu#3, lung CD103+ dendritic cells


title: B1b.PC#3

description: B1b.PC#3, B-1b, peritoneal cavity

source_name: Peritoneal Cavity

extract_protocol: Peritoneal cavity washout with 10ml of staining medium

value: CD3 Ly6c Ter119 Gr-1 CD11b

value: IgD+ IgM+ CD19+ CD43+ CD5+ CD45R+


title: B1b.PC#1

description: B1b.PC#1, B-1b, peritoneal cavity

value: 7 weeks

value: CD3 Ly6c Ter119 Gr-1 Mac1

value: IgD+ IgM+ CD19+ CD43+ CD5- CD45R+

value: dissection/trimming


title: B1a.Sp#2

description: B1a.Sp#2, B-1a, spleen

extract_protocol: Ground between 2 glass slides, ACK lysis of RBCs

value: male


title: B1a.PC#2

description: B1a.PC#2, B-1a, peritoneal cavity

value: CD3 Ly6c Ter119 Gr-1


title: DC.8+.MLN#1

description: DC.8+.MLN#1, mesenteric LN CD8+ dendritic cell

value: 6 weeks

value: PI SA-PECy7


title: B1a.PC#1

description: B1a.PC#1, B-1a, peritoneal cavity


title: B1a.Sp#1

description: B1a.Sp#1, B-1a, spleen


title: B1a.PC#3

description: B1a.PC#3, B-1a, peritoneal cavity


title: B.T3.Sp#2

description: B.T3.Sp#2, T3 (transitional)


title: B.T3.Sp#3

description: B.T3.Sp#3, T3 (transitional)


title: B.T3.Sp#1

description: B.T3.Sp#1, T3 (transitional)


title: B.T2.Sp#3

description: B.T2.Sp#3, T2 (transitional)


title: B.T1.Sp#3

description: B.T1.Sp#3, T1 (transitional)


title: B.T2.Sp#2

description: B.T2.Sp#2, T2 (transitional)


title: B1a.Sp#3

description: B1a.Sp#3, B-1a, spleen


title: B.T1.Sp#2

description: B.T1.Sp#2, T1 (transitional)


title: B1b.PC#2

description: B1b.PC#2, B-1b, peritoneal cavity


title: B.FrE.FL#3

description: B.FrE.FL#3, Fr. E (newly-formed B)

source_name: Fetal Liver

value: 18 days

value: both (pooled)


title: B.T2.Sp#1

description: B.T2.Sp#1, T2 (transitional)


title: Tgd.vg2-.Sp#3

status: Public on Dec 02 2009

description: Tgd.vg2-.Sp#3, SpleenVg2-, resting

extract_protocol: Glass Tissue Grinder  MACS depletion / Flow Sorting

value: 5 weeks

value: TCRd+ Vg2- CD44-


title: Tgd.vg2-.Sp#2

description: Tgd.vg2-.Sp#2, SpleenVg2-, resting


title: B.Fo.PC#1

description: B.Fo.PC#1, Fo-type, peritoneal cavity

value: IgD+ IgM+ CD19+ CD43- CD5- CD23+


title: B.FrE.FL#1

description: B.FrE.FL#1, Fr. E (newly-formed B)

extract_protocol: ground between 2 glass slides, ACK lysis of RBCs  1x flow sorting

value: Ter119 Ly6c CD11b Gr-1 CD3


title: Tgd.vg2-.act.Sp#2

description: Tgd.vg2-.act.Sp#2, SpleenVg2-, activated

value: TCRd+ Vg2- CD44+


title: Tgd.vg2-.Sp#1

description: Tgd.vg2-.Sp#1, SpleenVg2-, resting


title: Tgd.vg2-.act.Sp#3

description: Tgd.vg2-.act.Sp#3, SpleenVg2-, activated


title: Tgd.vg2-.act.Sp#1

description: Tgd.vg2-.act.Sp#1, SpleenVg2-, activated


title: Tgd.vg2+.act.Sp#2

description: Tgd.vg2+.act.Sp#2, SpleenVg2+, activated

value: TCRd+ Vg2+ CD44+


title: Tgd.vg2+.act.Sp#3

description: Tgd.vg2+.act.Sp#3, SpleenVg2+, activated


title: preB.FrC.BM#1

description: preB.FrC.BM#1, Fr. Cprime (cycling pre-B)

source_name: Bone marrow

extract_protocol: 1ml syringe disruption  Flow sorting

value: CD3 Ter119 Ly6c Cd11b Gr-1

value: CD19+ IgM- CD45R+ CD43+ HSA+


title: preB.FrD.BM#3

description: preB.FrD.BM#3, Fr D (pre-B)

extract_protocol: disruption by 1ml syringe, ACK lysis of RBCs

value: 8 weeks

value: CD3 Ly6c Ter119 Gr1 Mac1

value: CD19+ IgM- CD45R+ CD43-


title: B.T1.Sp#1

description: B.T1.Sp#1, T1 (transitional)

value: 7 weeks

value: CD3 Ly6c Ter119 Gr-1 Mac1

value: dissection/trimming

value: male


title: Tgd.vg2+.act.Sp#1

description: Tgd.vg2+.act.Sp#1, SpleenVg2+, activated


title: Tgd.vg3+24alo.e17.Th#3

description: Tgd.vg3+24alo.e17.Th#3, fetal thymus TCRd+ Vg3+ CD24-

source_name: fetal thymus

extract_protocol: Glass Tissue Grinder, Flow Sorting

value: 17 days

value: TCRd+ Vg3+ CD24-


title: B.FrE.FL#2

description: B.FrE.FL#2, Fr. E (newly-formed B)

extract_protocol: ground between 2 glass slides  1x flow sorting

value: 18 days

value: Ly6c Ter119 CD3 Gr-1 Cd11b

value: both (pooled)


title: Tgd.vg3+24alo.e17.Th#2

description: Tgd.vg3+24alo.e17.Th#2, fetal thymus TCRd+ Vg3+ CD24-


title: Tgd.vg3+24alo.e17.Th#1

description: Tgd.vg3+24alo.e17.Th#1, fetal thymus TCRd+ Vg3+ CD24-


title: B.Fo.PC#3

description: B.Fo.PC#3, Fo-type, peritoneal cavity

value: 10 weeks

value: CD3 Ly6c Ter119 Gr-1

value: IgD+ IgM+ CD19+ CD43- CD5- CD23+


title: Tgd.vg2+24ahi.e17.Th#1

description: Tgd.vg2+24ahi.e17.Th#1, fetal thymus TCRd+ Vg2+ CD24+

extract_protocol: Glass Tissue Grinder Flow Sorting

value: TCRd+ Vg2+ CD24+


title: Tgd.vg2+24ahi.e17.Th#3

description: Tgd.vg2+24ahi.e17.Th#3, fetal thymus TCRd+ Vg2+ CD24+


title: Tgd.vg2+24ahi.Th#3

description: Tgd.vg2+24ahi.Th#3, thymus TCRd+ Vg2+ CD24+

extract_protocol: Glass Tissue Grinder, MACS depletion / Flow Sorting

value: 5 weeks


title: B.FrF.BM#1

description: B.FrF.BM#1, Fr. F (recirc B)

value: 6 weeks

value: CD3 Ter119 Ly6c Cd11b Gr-1

value: CD19+ IgM+ AA4.1- HSA+


title: B.Fo.PC#2

description: B.Fo.PC#2, Fo-type, peritoneal cavity

value: 7 weeks


title: SC.STSL.BM#2

description: SC.STSL.BM#2, short-term reconstituting stem cell

value: Ly6c Ter119 GR1 CD11b CD3


title: Tgd.vg2+24ahi.Th#2

description: Tgd.vg2+24ahi.Th#2, thymus TCRd+ Vg2+ CD24+

value: dissection/trimming


title: B.FrE.BM#1

description: B.FrE.BM#1, Fr. E (newly-formed B)

value: CD19+ IgM+ AA4.1+ HSA+

value: male


title: Tgd.vg2+24ahi.e17.Th#2

description: Tgd.vg2+24ahi.e17.Th#2, fetal thymus TCRd+ Vg2+ CD24+

value: 17 days


title: Tgd.vg2+24ahi.Th#1

description: Tgd.vg2+24ahi.Th#1, thymus TCRd+ Vg2+ CD24+


title: SS patient number 43; diagnostic sample

status: Public on Sep 30 2009

type: genomic

city: Roma

first: Elisabetta

last: Caprini

state: Italy

address: Via dei Monti di Creta 104

country: Italy

institute: IDI-IRCCS

description:
Affymetrix 10K SNP genotype data
P43T

hyb_protocol: Affymetrix 10K mapping assay protocol.

scan_protocol: Affymetrix GeneChip scanner 3000-7G.

data_processing: GCOS, GTYPE. Genotype calling algorithm MPAM.

molecule: genomic DNA

organism: Homo sapiens

source_name: SS patient peripheral blood, CD3+ T lymphocytes

label_protocol: Affymetrix 10K mapping assay protocol.

growth_protocol: Not Applicable.

extract_protocol: DNA was prepared using standard proteinase K digestion and phenol/chloroform extraction.

treatment_protocol: Mononuclear cells were isolated from peripheral blood of patients with SS and either cryopreserved in liquid nitrogen or used immediately for CD3 positive selection and DNA extraction. Granulocyte fractions were separately collected, freezed or used immediately for DNA extraction.

tag: tissue

value: peripheral blood

tag: cell type

value: CD3+ T lymphocytes

tag: disease

value: Sézary Syndrome

tag: tumour type

value: Cutaneous T cell lymphoma


title: SS patient number 45; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P45T


title: SS patient number 48; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P48T


title: SS patient number 51; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P51T


title: SS patient number 49; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P49N

source_name: SS patient peripheral blood, granulocytes

value: granulocytes

value: Cutaneous T cell lymphoma, normal counterpart


title: SS patient number 48; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P48N


title: SS patient number 43; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P43N


title: SS patient number 51; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P51N


title: SS patient number 41; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P41N


title: SS patient number 45; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P45N


title: SS patient number 50; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P50T


title: SS patient number 50; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P50N


title: SS patient number 49; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P49T


title: SS patient number 42; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P42T


title: SS patient number 38; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P38T


title: SS patient number 39; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P39N


title: SS patient number 38; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P38N


title: SS patient number 42; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P42N


title: SS patient number 39; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P39T


title: SS patient number 35; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P35T


title: SS patient number 41; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P41T


title: SS patient number 37; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P37N


title: SS patient number 36; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P36N


title: SS patient number 37; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P37T


title: proB.FrBC.BM#2

description: proB.FrBC.BM#2, Fr. B/C (pro-B)


title: SS patient number 36; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P36T


title: SS patient number 34; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P34T


title: SS patient number 35; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P35N


title: SS patient number 32; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P32T


title: SS patient number 34; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P34N


title: SS patient number 27; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P27N


title: SS patient number 33; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P33N


title: SS patient number 28; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P28T


title: SS patient number 22; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P22T


title: SS patient number 32; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P32N


title: SS patient number 25; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P25T


title: SS patient number 30; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P30T


title: SS patient number 27; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P27T


title: SS patient number 33; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P33T


title: SS patient number 08; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P08N


title: SS patient number 30; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P30N


title: SS patient number 28; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P28N


title: SS patient number 11; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P11T


title: SS patient number 02; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P02N


title: SS patient number 23; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P23N


title: SS patient number 15; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P15T


title: SS patient number 02; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P02T


title: SS patient number 11; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P11N


title: SS patient number 25; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P25N


title: SS patient number 08; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P08T


title: SS patient number 05; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P05N


title: SS patient number 15; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P15N


title: SS patient number 22; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P22N


title: SS patient number 23; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P23T


title: SS patient number 22; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P22

hyb_protocol: Affymetrix HG-U133A assay protocol.

data_processing: R, Bioconductor. RMA was used for normalization.

label_protocol: Affymetrix HG-U133A assay protocol.

extract_protocol: Total RNA was extracted from sorted CD3+ T lymphocytes of SS patients using TRIzol Reagent according to manufacturer's instructions.

treatment_protocol: Mononuclear cells were isolated from peripheral blood of patients with SS and either cryopreserved in liquid nitrogen or used immediately for CD3 positive selection and RNA extraction.


title: SS patient number 43; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P43


title: SS patient number 26b; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P26b


title: SS patient number 05; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P05T


title: SS patient number 28; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P28


title: SS patient number 05; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P05


title: SS patient number 16; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P16


title: SS patient number 25; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P25


title: SS patient number 40; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P40


title: SS patient number 19; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P19


title: SS patient number 23; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P23


title: SS patient number 26; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P26


title: SS patient number 02; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P02


title: SS patient number 04; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P04


title: SS patient number 37; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P37


title: SS patient number 18; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P18


title: SS patient number 11; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P11


title: SS patient number 36; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P36


title: SS patient number 07; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P07


title: SS patient number 45; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P45


title: SS patient number 34; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P34


title: SS patient number 32; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P32


title: SS patient number 08; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P08


title: SS patient number 38; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P38


title: SS patient number 39; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P39


title: SS patient number 21; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P21


title: SS patient number 33; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P33


title: SS patient number 04b; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P04b


title: SS patient number 35; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P35


title: SS patient number 01; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P01


title: SS patient number 30; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P30


title: SS patient number 07; diagnostic sample

description:
Affymetrix 10K SNP genotype data
P07T


title: SS patient number 44; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P44


title: SS patient number 46; diagnostic sample; expression

description:
Gene expression data from SS patient peripheral blood.
P46


title: SS patient number 07; normal matched reference sample

description:
Affymetrix 10K SNP genotype data
P07N


title: CD4TESTJS#3

status: Public on May 16 2009

description: CD4 Test JS#3

extract_protocol: Glass slide teasing  Flow sorting


title: CD4TESTCJ#3

description: CD4 Test CJ#3


title: CD4TESTJS#1

description: CD4 Test JS#1


title: CD4Control#03

description: CD4 Control#3

extract_protocol: flow sorting


title: CD4Control#04

description: CD4 Control#4

extract_protocol: slide teasing

value: FACS


title: CD4TESTJS#2

description: CD4 Test JS#2


title: CD19Control#06

description: CD19 Control#6


title: CD4Control#01

description: CD4 Control#1


title: CD4TESTCJ#2

description: CD4 Test CJ#2


title: CD4TESTDB#1

description: CD4 Test DB#1


title: CD19Control#05

description: CD19 Control#5


title: preB.FrC.BM#2

status: Public on May 02 2009

description: preB.FrC.BM#2, Fr. Cprime (cycling pre-B)

extract_protocol: Tissue Disruption  Flow Sorting

value: CD19+ IgM- CD45R+ CD43+ HSA+


title: CD4TESTNA#1

description: CD4 Test NA#1

value: 6 weeks


title: CD4Control#02

description: CD4 Control#2


title: CD19Control#03

description: CD19 Control#3


title: preB.FrC.BM#3

description: preB.FrC.BM#3, Fr. Cprime (cycling pre-B)

value: 8 weeks

value: CD3 Ly6c Ter119 Gr1 Mac1


title: SC.STSL.BM#3

description: SC.STSL.BM#3, short-term reconstituting stem cell

extract_protocol: disruption by passing through 25g needle/1ml syringe, ACK lysis of RBCs  1x flow sorting

value: 11 weeks

value: Ly6c Ter119 CD11b CD3 GR1 IgM CD24


title: CD19Control#02

description: CD19 Control#2

value: dissection/trimming


title: CD19Control#04

description: CD19 Control#4


title: preB.FrD.BM#2

description: preB.FrD.BM#2, Fr D (pre-B)

value: CD3 Ter119 Ly6c Cd11b Gr-1

value: CD19+ IgM- CD45R+ CD43-


title: B.FrE.BM#3

description: B.FrE.BM#3, Fr. E (newly-formed B)

value: CD19+ IgM+ AA4.1+ HSA+

value: male


title: preB.FrD.BM#1

description: preB.FrD.BM#1, Fr D (pre-B)


title: B.FrF.BM#3

description: B.FrF.BM#3, Fr. F (recirc B)

value: CD19+ IgM+ AA4.1- HSA+


title: SC.STSL.BM#1

description: SC.STSL.BM#1, short-term reconstituting stem cell

value: 10 weeks


title: CD4Control#06

description: CD4 Control#6


title: CD19Control#01

description: CD19 Control#1


title: proB.FrBC.BM#1

description: proB.FrBC.BM#1, Fr. B/C (pro-B)

extract_protocol: Needle/Syringe  Flow sorting

value: Ter119 Ly6c CD3 Gr1 CD11b


title: CD4Control#05

description: CD4 Control#5


title: T.DPsm.Th#2

description: T.DPsm.Th#2, Double-Positive, Small Resting

extract_protocol: Glass Slide  Flow Sorting

value: 4+ 8+ TCR-/lo FSClo


title: T.DPsm.Th#1

description: T.DPsm.Th#1, Double-Positive, Small Resting


title: T.DPbl.Th#2

description: T.DPbl.Th#2, Double-Positive, Blasts

value: 4+ 8+ TCR-/lo FSChi


title: T.DPsm.Th#3

description: T.DPsm.Th#3, Double-Positive, Small Resting


title: T.DPbl.Th#3

description: T.DPbl.Th#3, Double-Positive, Blasts


title: T.DP69+.Th#2

description: T.DP69+.Th#2, Double-Positive, Early Positive Selection

value: 4+ 8+ TCRlo/int 69+


title: T.DP69+.Th#1

description: T.DP69+.Th#1, Double-Positive, Early Positive Selection


title: T.DPbl.Th#1

description: T.DPbl.Th#1, Double-Positive, Blasts


title: T.DP69+.Th#3

description: T.DP69+.Th#3, Double-Positive, Early Positive Selection


title: T.8SP69+.Th#2

description: T.8SP69+.Th#2, CD8 Single-Positive, Intermediate


title: T.8SP24int.Th#3

description: T.8SP24int.Th#3, CD8 Single-Positive, Semimature

value: 4- 8+ TCRhi 24int


title: T.8SP24int.Th#1

description: T.8SP24int.Th#1, CD8 Single-Positive, Semimature

value: 6 weeks


title: T.8SP24int.Th#2

description: T.8SP24int.Th#2, CD8 Single-Positive, Semimature


title: T.4SP69+.Th#3

description: T.4SP69+.Th#3, CD4 Single-Positive, Intermediate


title: B.FrE.BM#2

description: B.FrE.BM#2, Fr. E (newly-formed B)


title: T.4SP24int.Th#3

description: T.4SP24int.Th#3, CD4 Single-Positive, Semimature

value: 4+ 8- TCRhi 24int


title: T.4SP69+.Th#2

description: T.4SP69+.Th#2, CD4 Single-Positive, Intermediate


title: T.4SP69+.Th#1

description: T.4SP69+.Th#1, CD4 Single-Positive, Intermediate


title: T.4SP24-.Th#3

description: T.4SP24-.Th#3, CD4 Single-Positive, Mature


title: T.8SP69+.Th#1

description: T.8SP69+.Th#1, CD8 Single-Positive, Intermediate


title: T.4SP24int.Th#1

description: T.4SP24int.Th#1, CD4 Single-Positive, Semimature


title: T.4SP24int.Th#2

description: T.4SP24int.Th#2, CD4 Single-Positive, Semimature


title: T.4SP24-.Th#1

description: T.4SP24-.Th#1, CD4 Single-Positive, Mature


title: T.4SP24-.Th#2

description: T.4SP24-.Th#2, CD4 Single-Positive, Mature


title: T.4int8+.Th#1

description: T.4int8+.Th#1, Positive Selection, Intermediate

value: 4int 8+ TCRhi


title: T.4int8+.Th#3

description: T.4int8+.Th#3, Positive Selection, Intermediate


title: T.4FP3+25+.Sp#3

description: T.4FP3+25+.Sp#3, Spleen CD25+ Foxp3+ Tregs

extract_protocol: Glass Slide  Dynabeads/Flowsorting


title: T.8SP69+.Th#3

description: T.8SP69+.Th#3, CD8 Single-Positive, Intermediate


title: T.4+8int.Th#4

description: T.4+8int.Th#3, Positive Selection, Intermediate

extract_protocol: Glass Slide Flow Sorting

value: 4+ 8int TCRhi


title: T.4int8+.Th#2

description: T.4int8+.Th#2, Positive Selection, Intermediate


title: T.4FP3+25+.Sp#2

description: T.4FP3+25+.Sp#2, Spleen CD25+ Foxp3+ Tregs

extract_protocol: Glass Slide  Dynabeads/Flow Sorting


title: T.4+8int.Th#2

description: T.4+8int.Th#2, Positive Selection, Intermediate


title: T.4+8int.Th#1

description: T.4+8int.Th#1, Positive Selection, Intermediate


title: Th cells 1 week in culture 3

status: Public on May 24 2008

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description: no additional information

hyb_protocol: Total RNA was extracted using Trizol reagent (Invitrogen). RNA concentration, purity and integrity were assessed with Agilent 2100 Bioanalyzer, and the RNA 6000 Nano LabChip. Ten micrograms of total RNA was reverse-transcribed, followed by cDNA extraction using a PhaseLock gel (Eppendorf), and precipitation with ethanol and ammonium acetate. Biotinylated cRNA was in vitro transcribed using the MEGAscript high yield transcription kit (Ambion) according to the manufacturer's recommendations. Biotinylated cRNA was fragmented, and the hybridization cocktail was prepared according to Affymetrix protocols (15 µg fragmented biotin-labeled cRNA spiked with Eukaryotic Hybridization control). The Murine Genome 430A version 2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 oC for 16 h in a rotisserie motor, washed, and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400. Arrays were scanned on an Affymetrix GeneChip Scanner 3000 (MG430Av2 arrays).

data_processing: High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen); Data were analyzed using the Microarray Suite 5.0 software (Affymetrix). Microarrays were globally normalized and scaled to a trimmed mean expression value of 200. Quality checks were performed according to the manufacturer's recommendations. All arrays were compared to each other, and a relational database was generated using Microsoft Access software, including the following parameters: expression heights, call for presence of transcripts, p value for presence or absence of transcripts, log2 value of fold change and 95% confidence intervals, call for the significance of differentially expression, and the p value for that call. For each transcript the significance of differential expression between the groups of arrays was calculated using strict Bonferroni corrected Welch t-tests. Significantly differentially expressed genes were filtered according to the following criteria: mean fold change >= 2; difference of means >= 200; p-value <= 0,05; and immunoglobulin genes were excluded.

label: biotin

source_name: Th cells 1 week in culture 3

label_protocol: blocking: according to manufactures recommendations - probes were subsequently hybridised with the GeneChip 430A version 2 for 16 hrs at 45 oC- after washing the hybridisation signals were visualised by staining with streptavidin-phycoerythrin and amplification with an anti-streptavidin antibody

treatment_protocol: Naive CD4+CD62L+ Th lymphocytes from T cell receptor transgenic mice (DO11.10) were cultured in complete RPMI1640 (Invitrogen) supplemented with 10% heat-inactivated fetal calf serum, 100 units/ml penicillin, 0.1 mg/ml streptomycin, and 10 µM  -mercaptoethanol. Naive CD4+CD62L+ lymphocytes from 6-8 week old DO11.10 mice were isolated as described. Irradiated (30 Gy) BALB/c splenocytes were used as antigen-presenting cells (APC) at a ratio of 5:1. The cognate peptide ova323-339 (R. Volkmer-Engert, Humboldt University of Berlin, Berlin, Germany) was added at 0.5ßµM. For Th1 differentiation, cells were stimulated in the presence of 5 ng/ml recombinant murine IL-12 (R&D Systems) and 5 µg/ml anti-IL-4 antibody (11B11). Dead cells were removed by Ficoll-Histopaque separation. Every 6 days viable Th1 cells were harvested and restimulated under the original conditions, except that 10 ng/ml murine IL-2 (R&D Systems) was added.

tag: DO11.10 T cells towards Th1 direction


title: Th cells 4 weeks in culture 2

description: no additional information

source_name: Th cells 4 weeks in culture 2

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen). RNA concentration, purity and integrity were assessed with Agilent 2100 Bioanalyzer, and the RNA 6000 Nano LabChip. Ten micrograms of total RNA was reverse-transcribed, followed by cDNA extraction using a PhaseLock gel (Eppendorf), and precipitation with ethanol and ammonium acetate. Biotinylated cRNA was in vitro transcribed using the MEGAscript high yield transcription kit (Ambion) according to the manufacturer's recommendations. Biotinylated cRNA was fragmented, and the hybridization cocktail was prepared according to Affymetrix protocols (15 µg fragmented biotin-labeled cRNA spiked with Eukaryotic Hybridization control). The Murine Genome 430A version 2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 oC for 16 h in a rotisserie motor, washed, and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400. Arrays were scanned on an Affymetrix GeneChip Scanner 3000 (MG430Av2 arrays).


title: CD44highCD62L-CD25- CD4+ T cells from C57BL/6 murine bone marrow_rep3

status: Public on Apr 21 2009

description:
FACSAria sorted CD44highCD62L-CD25- CD4+ T cells of murine (C57BL/6 mice) bone marrow were compared to those of the spleen using Affymetrix GeneChip Mouse Genome 430A 2.0 Array. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the two groups to the GeneChip arrays.
Group of bone marrow chips: BMCD4T1, BMCD4T2, BMCD4T3.
Group of spleen chips: SCD4T1, SCD4T2, SCD4T3.

hyb_protocol: Biotinylated cRNA was in vitro transcribed using the MEGAscript high yield transcription kit (Ambion) according to the manufacturer's recommendations. Biotinylated cRNA was fragmented, and the hybridization cocktail was prepared according to Affymetrix protocols (15 µg fragmented biotin-labeled cRNA spiked with Eukaryotic hybridization controls). The Murine Genome 430A version 2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000

data_processing: Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PMID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 + 3 chips were compared to each other (bone marrow group vs. spleen, 9 comparisons, and all chips within the groups, twice 6 comparisons), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the calculated fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not with GCOS calculated – t tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t tests between 9 SLR values of bone marrow vs. spleen and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes were filtered using the both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009; PMID: 19265543.

label_protocol: 10 µg of total RNA from each cell sample was reverse transcribed using T7-(d)T24 primer and SuperScript II reverse transcriptase, following cDNA extraction with a PhaseLock gel (Eppendorf), and precipitation with ethanol and ammonium acetate. Blocking was according to manufactures recommendations and probes were subsequently hybridized. After washing the hybridization signals were visualized by staining with streptavidin-phycoerythrin and amplification with anti-streptavidin.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen). The amount, purity, and integrity of RNA was assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen). Ten micrograms of total RNA was reverse-transcribed, followed by cDNA extraction using a PhaseLock gel (Eppendorf), and precipitation with ethanol and ammonium acetate.

treatment_protocol: CD44highCD62L-CD25- CD4+ T cells from spleen or bone marrow of 12-16 week old C57BL/6 mice were sorted with FACSAria

value: CD44highCD62L-CD25- CD4+ T cells

value: bone marrow


title: Control virus for twist overexpression 1

description: no additional information

data_processing:
Data were analyzed using High Performance Chip Data Analysis (HPCDA, unpublished, Dr. Joachim R. Grün);
Data were analyzed using the Microarray Suite 5.0 software (Affymetrix). Microarrays were globally normalized and scaled to a trimmed mean expression value of 200. Quality checks were performed according to the manufacturer's recommendations. All arrays were compared to each other, and a relational database was generated using Microsoft Access software, including the following parameters: expression heights, call for presence of transcripts, p value for presence or absence of transcripts, log2 value of fold change and 95% confidence intervals, call for the significance of differentially expression, and the p value for that call. For each transcript the significance of differential expression between the groups of arrays was calculated using strict Bonferroni corrected Welch t-tests. Significantly differentially expressed genes were filtered according to the following criteria: mean fold change >= 1,5; difference of means >= 200; p-value <= 0,05; and immunoglobulin genes were excluded.

growth_protocol: Genes differentially expressed upon ectopic twist1 overexpression. Splenic DO11.10 cells were activated in vitro with the cognate peptide ova327-339 in the presence of 1ng/ml IL-12 and 1ng/ml IL-2. On day 2 cells were infected with control virus, or twist1-encoding virus. On day 5 cells were sorted according to expression of the viral marker gene gfp. Cells were restimulated for four hours with PMA/ionomycin. The transcriptional profiles of duplicates of cultures were compared using Affymetrix Murine Genome (MG) 430A 2.0 GeneChip arrays. - 10 µg of total RNA from each cell sample was reverse transcribed using T7-(d)T24 primer and SuperScript II reverse transcriptase- cDNA extraction with a PhaseLock gel (Eppendorf), and precipitation with ethanol and ammonium acetate- Biotinylated cRNA was transcribed with the MEGAscript high yield transcription kit (Ambion), fragmented, and the hybridization cocktail was prepared (15 µg fragmented biotin-labeled cRNA spiked with Eukaryotic Hybridization control)- probes were subsequently hybridised with the GeneChip 430A version 2 for 16 hrs at 45oC- after washing the hybridisation signals were visualised by staining with streptavidin-phycoerythrin and amplification with an anti-streptavidin antibody- emptyExp.3_2004-05-25; emptyExp.4_2004-05-25 - twistExp.3_2004-05-25; twistExp.4_2004-05-25- empty: cells infected with control retrovirus- twist: cells infected with retrovirus, encoding twist1- Exp.3-4: Culture/Exp. No.Two arrays per group representing two independent cultures.

treatment_protocol: Lymphocytes were cultured in complete RPMI1640 (Invitrogen) supplemented with 10% heat-inactivated fetal calf serum, 100 units/ml penicillin, 0.1 mg/ml streptomycin and 10 µM  -mercaptoethanol. Na ve CD4+CD62L+ lymphocytes from 6-8 week old DO11.10 mice were isolated and irradiated (30 Gy) BALB/c splenocytes were used as antigen-presenting cells (APC) at a ratio of 5:1. The cognate peptide ova323-339 (R. Volkmer-Engert, Humboldt University of Berlin, Berlin, Germany) was added at 0.5ßµM. For Th1 differentiation, cells were stimulated in the presence of 1 ng/ml recombinat murine IL-12 and 1 ng/ml recombinant murine IL-2 (R&D Systems). Dead cells were removed by Ficoll-Histopaque separation. For retroviral overexpression the vector GFP-RV was used, kindly provided by K Murphy (Howard Hughes Medical Institute, St. Louis, Missouri). The complete coding sequence for murine twist1 (IMAGE cDNA clone; Accession ID: BC033434-NCBI) was amplified by PCR. BglII and XhoI-compatible restriction sites were introduced by the PCR primers for cloning into the unique sites of the vector upstream of the internal ribosome entry site (IRES)-gfp cassette. The accuracy of cloning steps was confirmed by DNA sequencing. Retroviral stocks were obtained by calcium phosphate co-transfection of HEK293 cells with the retrovirus packaging plasmids pECO and pCGP. The medium was replaced after 4 h, and viral supernatants were collected 48 h later. Th cells were infected 40 h after activation by 60 min centrifugation at 1300g at 3ï °C with viral supernatant and 8mg/ml polybrene, followed by 1 h at 37 °C, and replacement of the viral supernatant with the former culture supernatant.

tag: Splenic DO11.10 cells


title: Th cells 1 week in culture 2

description: no additional information

source_name: Th cells 1 week in culture 2


title: CD44highCD62L-CD25- CD4+ T cells from C57BL/6 murine spleen_rep3

value: spleen


title: CD44highCD62L-CD25- CD4+ T cells from C57BL/6 murine bone marrow_rep2


title: CD44highCD62L-CD25- CD4+ T cells from C57BL/6 murine spleen_rep2


title: Th cells 4 weeks in culture 3

description: no additional information

source_name: Th cells 4 weeks in culture 3


title: Twist overexpression 2

description: no additional information

source_name: Twist overexpression 2


title: Th cells 4 weeks in culture 1

description: no additional information

source_name: Th cells 4 weeks in culture 1


title: Twist overexpression 1

description: no additional information

source_name: Twist overexpression 1


title: CD44highCD62L-CD25- CD4+ T cells from C57BL/6 murine spleen_rep1


title: CD44highCD62L-CD25- CD4+ T cells from C57BL/6 murine bone marrow_rep1


title: Affy2H1 (D7)

status: Public on Aug 30 2005

description: 1st hybridization of genostem7 sample on new  microarray2

data_processing: Affymetrix GCOS/ Rosetta Resolver V5.0

label: Streptavidin Phycoerythrin

source_name: hybridization1 of genostem7 on new chip

tag: new chip


title: Affy1H2 (MO27_4)

description: 1st re-hybridization (2nd hybridization) of genostem1 sample on stripped microarray2

source_name: hybridization2 of genostem1 (D3) on stripped chip

tag: rehybridization (D3) of stripped array1 (MO27_4)


title: Affy2H2 (MO28_4)

description: 1st re-hybridization (2nd hybridization) of genostem7 sample on stripped microarray1

source_name: hybridization2 of genostem7 (D7) on stripped chip

tag: rehybridization (D7) of stripped array2 (MO28_4)


title: B.FrF.BM#2

description: B.FrF.BM#2, Fr. F (recirc B)

value: CD3 Ter119 Ly6c Cd11b Gr-1

value: dissection/trimming


title: Rat3 LURA rep2

status: Public on Dec 18 2008

city: Pittsburgh

first: Wei

last: Wu

state: PA

address: MUH 628 NW, 3459 Fifth Ave

department: Medicine/PACCM

institute: University of Pittsburgh

hyb_protocol: According to standard CodeLink protocols; see details at http://www1.gelifesciences.com/APTRIX/upp00919.nsf/Content/WD%3ACodeLink+Gene+E%28281090525-B500%29?OpenDocument&hometitle=WebDocs

scan_protocol: Microarray slides were scanned using a GenePix Array Scanner. For details, see the protocol at http://www1.gelifesciences.com/APTRIX/upp00919.nsf/Content/WD%3ACodeLink+Gene+E%28281090525-B500%29?OpenDocument&hometitle=WebDocs

data_processing: The raw intensity values were normalized by the CyclicLoess normalization method as described in Wu W, et. al, BMC Bioinformatics. 2005 Dec 28;6:309. The data was also preprocessed and postprocessed using the protocol described in the same paper and the submitted paper.

organism: Rattus norvegicus

source_name: lung tissue

label_protocol: Briefly, the RNAs extracted from whole lung tissue of each rat (mixed with spiked-in bacterial RNAs served as positive controls) were reverse transcribed into double stranded cDNAs; then the cDNAs were amplified into cRNAs by in vitro transcription. The cRNAs were labeled with a red (Cy5) fluorescent dye and hybridized to a CodeLink Bioarray which is presynthesized with probes.

growth_protocol: Adult inbred Sprague-Dawley male rats (weights: 250-275g) were placed in chambers in which oxygen and carbon dioxide concentrations were carefully monitored and controlled.

extract_protocol: To prepare RNAs for microarray experiments and quantitative RT-PCRs, 1 ml per 50 mg of frozen lung tissues were homogenized in ice cold Trizol, and phase separated with Chlorophorm (0.2ml per 1ml Trisol reagent). The RNAs were precipitated from the aqueous phase using Isopropanol (0.5ml per 1ml Trisol). The RNA pallet then was washed with 75%Ethanol. Next the extracted RNAs were purified further using the RNeasy Mini Cleanup protocol (Qiagen 74104) according to the manufacturer’s recommendations. The quantities of RNAs were determined by OD measurements at 260nm, and their qualities were assessed by Agilent Bioanalyzer and by running the RNAs on formamide formaldehyde denaturing gels

treatment_protocol: Rats subject to the intermittent hypoxia (IH) treatment were exposed to 90 second cycles of 10% inspired oxygen followed by 90 seconds of 21% inspired oxygen for 12 hours of simulated daylight when rats sleep; for the remaining 12 hours during the night, the rats were exposed to 21% inspired oxygen.  Rats subject to the sustained hypoxia (SH) treatment were exposed to 10% inspired oxygen at all times. Time sacrifices of these rats exposed to IH and SH respectively were performed on days 1, 3, 7, 14, and 30.

tag: exposed to room air


title: Th cells 1 week in culture 1

description: no additional information

source_name: Th cells 1 week in culture 1


title: Control virus for twist overexpression 2

description: no additional information


title: Affy1H1 (D3)

description: 1st hybridization of genostem1 sample on new  microarray1

source_name: hybridization1 of genostem1 on new chip