Experiment section domain ebi.ac.uk accession E-TABM-102 quality_control biological_replicate experiment_design_type "compound_treatment_design,genetic_modification_design,time_series_design" name "Transcription profiling of wild-type and ATF3 -/-mouse bone marrow macrophages stimulated with lipopolysaccharide after 1, 2, 4, 8 and 24 hours" description Time course data from lipopolysaccharide-stimulated wild-type and ATF3 -/- mouse bone marrow macrophages were collected to investigate the transcriptional network in Toll-like recepter 4-activated macrophages. release_date 2006-05-30 submission_date 2006-05-30 submitter Bruz Marzolf organization Institute for Systems Biology publication_title Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4 authors Mark Gilchrist; Vesteinn Thorsson; Bin Li; Alistair G. Rust; Martin Korb; Kathleen Kennedy; Tsonwin Hai; Hamid Bolouri and Alan Aderem journal Nature volume 441 issue 2006 May 11 pages 173-178 year 2006 Protocol section accession text name type P-TABM-gilchrist1 "Flush femurs from C57BL/6 mice (Jackson Laboratories) with complete RPMI (RPMI 1640 supplemented with 10% FCS, 2mM L-glutamine, 100 IU/mL penicillin and 100ug/mL streptomycin, all from Cellgro, Mediatech, except the FCS which is from from Hyclone). Plate bone marrow cells on non-tissue culture treated plastic in complete RPMI supplemented with recombinant human M-CSF (rhM-CSF) at 50 ng/mL (Chiron). On day 3, wash the cells two times with complete RPMI and then grow for 4 more days in complete RPMI supplemented with 50 ng/mL of rhM-CSF." Bone marrow macrophage growth grow P-TABM-gilchrist2 "On day 7, stimulate the cells with 10 ng/mL lipopolysaccharide (S. Minnesota, List) for 1, 2, 4, 8 and 24 hours without changing the media." Bone marrow macrophage stimulation treatment Hybridization section File[raw] File[normalized] File[exp] File[cdf] Array[accession] Array[serial] Protocol[grow] Protocol[treatment] Protocol[extraction] Protocol[labeling] BioSource BioSourceMaterial BioMaterialCharacteristics[Organism] BioMaterialCharacteristics[StrainOrLine] BiomaterialCharacteristics[Genotype] BioMaterialCharacteristics[Sex] BioMaterialCharacteristics[CellType] BioMaterialCharacteristics[GeneticModification] FactorValue[Compound] FactorValue[Dose(ng/mL)] FactorValue[Time(h)] FactorValue[Genotype] 20040603_03_LPS1-0.CEL 20040603_03_LPS1-0.CHP 20040603_03_LPS1-0.EXP Mouse430_2.cdf A-AFFY-45 4001319 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 0 hr Mouse 1 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage none 0 0 wild_type 20040621_01_LPS2-0.CEL 20040621_01_LPS2-0.CHP 20040621_01_LPS2-0.EXP Mouse430_2.cdf A-AFFY-45 4001319 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 0 hr Mouse 2 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage none 0 0 wild_type 20040622_01_LPS3-0.CEL 20040622_01_LPS3-0.CHP 20040622_01_LPS3-0.EXP Mouse430_2.cdf A-AFFY-45 4001319 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 0 hr Mouse 3 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage none 0 0 wild_type 20040609_03_LPS1-60.CEL 20040609_03_LPS1-60.CHP 20040609_03_LPS1-60.EXP Mouse430_2.cdf A-AFFY-45 4001319 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 1 hr Mouse 1 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 1 wild_type 20040621_04_LPS2-60.CEL 20040621_04_LPS2-60.CHP 20040621_04_LPS2-60.EXP Mouse430_2.cdf A-AFFY-45 4001319 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 1 hr Mouse 2 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 1 wild_type 20040622_04_LPS3-60.CEL 20040622_04_LPS3-60.CHP 20040622_04_LPS3-60.EXP Mouse430_2.cdf A-AFFY-45 4001789 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 1 hr Mouse 3 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 1 wild_type 20040603_04_LPS1-120.CEL 20040603_04_LPS1-120.CHP 20040603_04_LPS1-120.EXP Mouse430_2.cdf A-AFFY-45 4001319 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 2 hr Mouse 1 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 2 wild_type 20040621_06_LPS2-120.CEL 20040621_06_LPS2-120.CHP 20040621_06_LPS2-120.EXP Mouse430_2.cdf A-AFFY-45 4001319 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 2 hr Mouse 2 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 2 wild_type 20040622_06_LPS3-120.CEL 20040622_06_LPS3-120.CHP 20040622_06_LPS3-120.EXP Mouse430_2.cdf A-AFFY-45 4001789 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 2 hr Mouse 3 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 2 wild_type 20050310_03_C57_A-240.CEL 20050310_03_C57_A-240.CHP 20050310_03_C57_A-240.EXP Mouse430_2.cdf A-AFFY-45 4005732 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 4 hr Mouse 1 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 4 wild_type 20050505_09_C57_LPS_B_240.CEL 20050505_09_C57_LPS_B_240.CHP 20050505_09_C57_LPS_B_240.EXP Mouse430_2.cdf A-AFFY-45 4006289 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 4 hr Mouse 2 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 4 wild_type 20050623_03_C57_LPS_C_240min.CEL 20050623_03_C57_LPS_C_240min.CHP 20050623_03_C57_LPS_C_240min.EXP Mouse430_2.cdf A-AFFY-45 4005732 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 4 hr Mouse 3 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 4 wild_type 20050622_09_LPS_A1_8_hr.CEL 20050622_09_LPS_A1_8_hr.CHP 20050622_09_LPS_A1_8_hr.EXP Mouse430_2.cdf A-AFFY-45 4009043 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 8 hr Mouse 1 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 8 wild_type 20050622_11_LPS_B1_8_hr.CEL 20050622_11_LPS_B1_8_hr.CHP 20050622_11_LPS_B1_8_hr.EXP Mouse430_2.cdf A-AFFY-45 4005732 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 8 hr Mouse 2 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 8 wild_type 20050623_01_LPS_C1_8hr.CEL 20050623_01_LPS_C1_8hr.CHP 20050623_01_LPS_C1_8hr.EXP Mouse430_2.cdf A-AFFY-45 4006263 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 8 hr Mouse 3 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 8 wild_type 20050622_10_LPS_A1_24_hr.CEL 20050622_10_LPS_A1_24_hr.CHP 20050622_10_LPS_A1_24_hr.EXP Mouse430_2.cdf A-AFFY-45 4009043 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 24 hr Mouse 1 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 24 wild_type 20050622_12_LPS_B1_24_hr.CEL 20050622_12_LPS_B1_24_hr.CHP 20050622_12_LPS_B1_24_hr.EXP Mouse430_2.cdf A-AFFY-45 4005732 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 24 hr Mouse 2 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 24 wild_type 20050623_04_LPS_C2_24hr.CEL 20050623_04_LPS_C2_24hr.CHP 20050623_04_LPS_C2_24hr.EXP Mouse430_2.cdf A-AFFY-45 4005732 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 LPS 24 hr Mouse 3 cell Mus musculus C57BL/6 wild_type mixed_sex macrophage lipopolysaccharide 10 24 wild_type 20050310_04_ATF3--_A-0.CEL 20050310_04_ATF3--_A-0.CHP 20050310_04_ATF3--_A-0.EXP Mouse430_2.cdf A-AFFY-45 4005732 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 ATF3 -/- LPS 0 hr Mouse 1 cell Mus musculus ATF3 -/- C57BL/6 ATF3 -/- mixed_sex macrophage gene_knock_out none 0 0 ATF3-/- 20050331_08_ATF3--_B-0.CEL 20050331_08_ATF3--_B-0.CHP 20050331_08_ATF3--_B-0.EXP Mouse430_2.cdf A-AFFY-45 4006290 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 ATF3 -/- LPS 0 hr Mouse 2 cell Mus musculus ATF3 -/- C57BL/6 ATF3 -/- mixed_sex macrophage gene_knock_out none 0 0 ATF3-/- 20050504_09_ATF3_LPS_E-0.CEL 20050504_09_ATF3_LPS_E-0.CHP 20050504_09_ATF3_LPS_E-0.EXP Mouse430_2.cdf A-AFFY-45 4006289 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 ATF3 -/- LPS 0 hr Mouse 3 cell Mus musculus ATF3 -/- C57BL/6 ATF3 -/- mixed_sex macrophage gene_knock_out none 0 0 ATF3-/- 20050310_05_ATF3--_A-60.CEL 20050310_05_ATF3--_A-60.CHP 20050310_05_ATF3--_A-60.EXP Mouse430_2.cdf A-AFFY-45 4005732 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 ATF3 -/- LPS 1 hr Mouse 1 cell Mus musculus ATF3 -/- C57BL/6 ATF3 -/- mixed_sex macrophage gene_knock_out lipopolysaccharide 10 1 ATF3-/- 20050411_04_ATF3--_B-60.CEL 20050411_04_ATF3--_B-60.CHP 20050411_04_ATF3--_B-60.EXP Mouse430_2.cdf A-AFFY-45 4006290 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 ATF3 -/- LPS 1 hr Mouse 2 cell Mus musculus ATF3 -/- C57BL/6 ATF3 -/- mixed_sex macrophage gene_knock_out lipopolysaccharide 10 1 ATF3-/- 20050504_10_ATF3_LPS_E-60.CEL 20050504_10_ATF3_LPS_E-60.CHP 20050504_10_ATF3_LPS_E-60.EXP Mouse430_2.cdf A-AFFY-45 4006289 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 ATF3 -/- LPS 1 hr Mouse 3 cell Mus musculus ATF3 -/- C57BL/6 ATF3 -/- mixed_sex macrophage gene_knock_out lipopolysaccharide 10 1 ATF3-/- 20050310_06_ATF3--_A-120.CEL 20050310_06_ATF3--_A-120.CHP 20050310_06_ATF3--_A-120.EXP Mouse430_2.cdf A-AFFY-45 4005732 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 ATF3 -/- LPS 2 hr Mouse 1 cell Mus musculus ATF3 -/- C57BL/6 ATF3 -/- mixed_sex macrophage gene_knock_out lipopolysaccharide 10 2 ATF3-/- 20050411_05_ATF3--_B-120.CEL 20050411_05_ATF3--_B-120.CHP 20050411_05_ATF3--_B-120.EXP Mouse430_2.cdf A-AFFY-45 4006290 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 ATF3 -/- LPS 2 hr Mouse 2 cell Mus musculus ATF3 -/- C57BL/6 ATF3 -/- mixed_sex macrophage gene_knock_out lipopolysaccharide 10 2 ATF3-/- 20050504_11_ATF3_LPS_E-120.CEL 20050504_11_ATF3_LPS_E-120.CHP 20050504_11_ATF3_LPS_E-120.EXP Mouse430_2.cdf A-AFFY-45 4006289 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 ATF3 -/- LPS 2 hr Mouse 3 cell Mus musculus ATF3 -/- C57BL/6 ATF3 -/- mixed_sex macrophage gene_knock_out lipopolysaccharide 10 2 ATF3-/- 20050310_07_ATF3--_A-240.CEL 20050310_07_ATF3--_A-240.CHP 20050310_07_ATF3--_A-240.EXP Mouse430_2.cdf A-AFFY-45 4005732 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 ATF3 -/- LPS 4 hr Mouse 1 cell Mus musculus ATF3 -/- C57BL/6 ATF3 -/- mixed_sex macrophage gene_knock_out lipopolysaccharide 10 4 ATF3-/- 20050623_02_ATF3_B_240min.CEL 20050623_02_ATF3_B_240min.CHP 20050623_02_ATF3_B_240min.EXP Mouse430_2.cdf A-AFFY-45 4006263 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 ATF3 -/- LPS 4 hr Mouse 2 cell Mus musculus ATF3 -/- C57BL/6 ATF3 -/- mixed_sex macrophage gene_knock_out lipopolysaccharide 10 4 ATF3-/- 20050504_12_ATF3_LPS_E-240.CEL 20050504_12_ATF3_LPS_E-240.CHP 20050504_12_ATF3_LPS_E-240.EXP Mouse430_2.cdf A-AFFY-45 4006289 P-TABM-gilchrist1 P-TABM-gilchrist2 P-AFFY-1 P-AFFY-2 ATF3 -/- LPS 4 hr Mouse 3 cell Mus musculus ATF3 -/- C57BL/6 ATF3 -/- mixed_sex macrophage gene_knock_out lipopolysaccharide 10 4 ATF3-/-