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{{f5samples
{{f5samples
|id=FF:10823-111C4
|F5samples=
|name=B lymphoblastoid cell line: GM12878 ENCODE, biol_rep3
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|sample_id=10823
|rna_tube_id=111C4
|rna_box=111
|rna_position=C4
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=
|sample_strain=
|sample_dev_stage=
|sample_tissue=blood
|sample_donor(cell lot)=
|sample_sex=female
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=2.19
|rna_od260/280=2.02
|sample_cell_type=b cell
|sample_cell_line=GM12878
|sample_collaboration=Carrie Davis (Cold spring Harbor Laboratories)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=35.347
|rna_concentration=0.70694
|sample_note=
|profile_hcage=CNhs12333,LSID913,release011,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000826,CL:0000837,CL:0000838,CL:0000945,CL:0000988,CL:0002031,CL:0002032,CL:0002087,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000826,CL:0000837,CL:0000838,CL:0000945,CL:0000988,CL:0002031,CL:0002032,CL:0002087,CL:0002320,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0101035,FF:0101522
|fonse_cell_line=FF:0101035,FF:0101522
|fonse_cell_line_closure=FF:0101035,FF:0101522
|fonse_cell_line_closure=FF:0101035,FF:0101522
Line 66: Line 34:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=POU2F1..3:2.37041826617;POU5F1:2.19357996837;HOXA9_MEIS1:1.9820005443;DMAP1_NCOR{1,2}_SMARC:1.93753310364;NFKB1_REL_RELA:1.88454308597;PAX6:1.83815824765;E2F1..5:1.66746562237;NFY{A,B,C}:1.61773653537;PDX1:1.61324370331;MYB:1.60991349116;IRF7:1.57365992701;ELF1,2,4:1.5678364964;IRF1,2:1.51029513615;ELK1,4_GABP{A,B1}:1.50927736904;AIRE:1.49872807127;NKX6-1,2:1.40257422802;PITX1..3:1.34016609735;TOPORS:1.27979895404;SPI1:1.09819733832;YY1:1.09624363262;VSX1,2:1.09189264097;HIF1A:1.00233337086;RUNX1..3:0.958333536542;FOXA2:0.938267184563;CDX1,2,4:0.932634597613;NRF1:0.917827322361;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.874782217273;PAX3,7:0.867746317015;PAX8:0.834739262651;ZBTB16:0.747432493176;SPIB:0.743488815208;ZNF143:0.740075913508;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.731695537187;POU1F1:0.679921587167;RBPJ:0.675027664415;AHR_ARNT_ARNT2:0.645625869143;ETS1,2:0.643138666976;OCT4_SOX2{dimer}:0.616760528987;MYOD1:0.564347942058;EVI1:0.517866932713;FOXP3:0.51314630871;BREu{core}:0.483195567593;HNF4A_NR2F1,2:0.481010213497;LMO2:0.45816833409;POU3F1..4:0.451495795201;SNAI1..3:0.445885606129;NR5A1,2:0.441842885738;GFI1:0.425449336341;FOXP1:0.420256678772;SPZ1:0.416396655147;NKX2-2,8:0.413254415911;ZNF384:0.398427782303;ZEB1:0.393141169649;CUX2:0.367008262589;ESRRA:0.34488416334;RORA:0.341468289947;PBX1:0.327464552073;HNF1A:0.318475029335;ARID5B:0.299849604422;FOXN1:0.283588409682;CDC5L:0.219548502348;HSF1,2:0.217125661908;NANOG{mouse}:0.212561126276;GATA6:0.185705424925;STAT1,3:0.181699498951;RFX2..5_RFXANK_RFXAP:0.181529364036;ALX4:0.175426672194;FOX{F1,F2,J1}:0.172798725348;SOX{8,9,10}:0.156916122192;ATF5_CREB3:0.11407071491;TGIF1:0.0970735125656;ESR1:0.0885747640974;CRX:0.0790686360018;IKZF2:0.078620757849;PRRX1,2:0.0757602491704;LHX3,4:0.0731297292607;TFDP1:0.0592301017446;RXRA_VDR{dimer}:0.0524905420829;PAX2:0.0243553982515;NKX3-2:-0.00946612243698;HES1:-0.0103882197375;TP53:-0.0248525305369;CREB1:-0.0915954864285;PRDM1:-0.112168379044;bHLH_family:-0.141380649767;NKX2-3_NKX2-5:-0.145715604126;FOXQ1:-0.146672303626;EBF1:-0.152619767882;SOX5:-0.171044940095;NR1H4:-0.171457310599;PAX4:-0.202124160018;NFE2:-0.229810458963;ATF4:-0.230366473365;DBP:-0.237831449627;TLX2:-0.241852673121;MEF2{A,B,C,D}:-0.249252057959;LEF1_TCF7_TCF7L1,2:-0.278211047761;BPTF:-0.296763365785;HAND1,2:-0.304390242869;SRF:-0.334628178397;EP300:-0.390234042756;ALX1:-0.391391531104;GATA4:-0.413959866104;HOX{A5,B5}:-0.418150119657;ADNP_IRX_SIX_ZHX:-0.43834722201;HBP1_HMGB_SSRP1_UBTF:-0.442831407362;HOX{A4,D4}:-0.446136280294;NFATC1..3:-0.469194168639;FOS_FOS{B,L1}_JUN{B,D}:-0.47580072585;RXR{A,B,G}:-0.487865268285;TEF:-0.493257045261;AR:-0.505828926121;GFI1B:-0.511146385668;SOX17:-0.519680026523;NR6A1:-0.550791796542;SOX2:-0.560507912013;KLF4:-0.584431356653;FOSL2:-0.58658511533;NKX2-1,4:-0.592512316824;ONECUT1,2:-0.603083014679;BACH2:-0.606519400499;HMGA1,2:-0.618924271622;ZFP161:-0.639488788223;UFEwm:-0.640450560739;EN1,2:-0.64289009084;STAT2,4,6:-0.657564393;IKZF1:-0.682032376795;RREB1:-0.685940158176;CEBPA,B_DDIT3:-0.688195997655;NFIL3:-0.699361114087;GLI1..3:-0.734260517816;MZF1:-0.739685154939;TFAP4:-0.74098921276;SMAD1..7,9:-0.754455638358;MYBL2:-0.766991593172;STAT5{A,B}:-0.782479505782;GCM1,2:-0.784829374914;HOX{A6,A7,B6,B7}:-0.803687033526;NKX3-1:-0.818993250626;PPARG:-0.82056527378;PAX1,9:-0.826713516328;SREBF1,2:-0.836657185559;ATF2:-0.843870436334;HLF:-0.846440132248;NHLH1,2:-0.861330245316;TAL1_TCF{3,4,12}:-0.914148726196;ZNF148:-0.923810945583;MYFfamily:-0.924009766946;FOXD3:-0.928959043952;ZNF423:-0.957188083363;MTF1:-0.963145026819;EGR1..3:-0.977760003256;ZIC1..3:-0.992846577728;RFX1:-1.01291870628;XCPE1{core}:-1.03851626774;FOXO1,3,4:-1.0471811307;MTE{core}:-1.06487027425;TBP:-1.08372042353;HIC1:-1.08986749596;JUN:-1.1058763335;T:-1.12366012248;REST:-1.13330000012;NFIX:-1.14587520621;PAX5:-1.15753204538;GTF2I:-1.18459570894;NFE2L2:-1.21223264823;XBP1:-1.23331964364;NFE2L1:-1.24787716658;MAFB:-1.27537639605;MED-1{core}:-1.2857994497;FOXM1:-1.2922012403;NANOG:-1.30990483605;TFAP2{A,C}:-1.32150589921;PATZ1:-1.34822630122;TFCP2:-1.35779454385;ATF6:-1.37025780055;GTF2A1,2:-1.38000243687;HMX1:-1.388945926;GZF1:-1.43654812128;TBX4,5:-1.46044857331;MAZ:-1.47340187805;ZNF238:-1.47592322241;TLX1..3_NFIC{dimer}:-1.48167347747;ZBTB6:-1.63966328517;POU6F1:-1.67507898292;TEAD1:-1.68001545219;NR3C1:-1.68460187491;FOX{D1,D2}:-1.72871992526;SP1:-1.81297752058;TFAP2B:-1.90774420056;FOX{I1,J2}:-2.13253849766;FOXL1:-2.4673002322
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10823-111C4
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102062
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102062
|name=B lymphoblastoid cell line: GM12878 ENCODE, biol_rep3
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12333,LSID913,release011,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=111
|rna_catalog_number=
|rna_concentration=0.70694
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.19
|rna_od260/280=2.02
|rna_position=C4
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=111C4
|rna_weight_ug=35.347
|sample_age=
|sample_cell_catalog=
|sample_cell_line=GM12878
|sample_cell_lot=
|sample_cell_type=b cell
|sample_collaboration=Carrie Davis (Cold spring Harbor Laboratories)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10823
|sample_note=
|sample_sex=female
|sample_species=
|sample_strain=
|sample_tissue=blood
|top_motifs=POU2F1..3:2.37041826617;POU5F1:2.19357996837;HOXA9_MEIS1:1.9820005443;DMAP1_NCOR{1,2}_SMARC:1.93753310364;NFKB1_REL_RELA:1.88454308597;PAX6:1.83815824765;E2F1..5:1.66746562237;NFY{A,B,C}:1.61773653537;PDX1:1.61324370331;MYB:1.60991349116;IRF7:1.57365992701;ELF1,2,4:1.5678364964;IRF1,2:1.51029513615;ELK1,4_GABP{A,B1}:1.50927736904;AIRE:1.49872807127;NKX6-1,2:1.40257422802;PITX1..3:1.34016609735;TOPORS:1.27979895404;SPI1:1.09819733832;YY1:1.09624363262;VSX1,2:1.09189264097;HIF1A:1.00233337086;RUNX1..3:0.958333536542;FOXA2:0.938267184563;CDX1,2,4:0.932634597613;NRF1:0.917827322361;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.874782217273;PAX3,7:0.867746317015;PAX8:0.834739262651;ZBTB16:0.747432493176;SPIB:0.743488815208;ZNF143:0.740075913508;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.731695537187;POU1F1:0.679921587167;RBPJ:0.675027664415;AHR_ARNT_ARNT2:0.645625869143;ETS1,2:0.643138666976;OCT4_SOX2{dimer}:0.616760528987;MYOD1:0.564347942058;EVI1:0.517866932713;FOXP3:0.51314630871;BREu{core}:0.483195567593;HNF4A_NR2F1,2:0.481010213497;LMO2:0.45816833409;POU3F1..4:0.451495795201;SNAI1..3:0.445885606129;NR5A1,2:0.441842885738;GFI1:0.425449336341;FOXP1:0.420256678772;SPZ1:0.416396655147;NKX2-2,8:0.413254415911;ZNF384:0.398427782303;ZEB1:0.393141169649;CUX2:0.367008262589;ESRRA:0.34488416334;RORA:0.341468289947;PBX1:0.327464552073;HNF1A:0.318475029335;ARID5B:0.299849604422;FOXN1:0.283588409682;CDC5L:0.219548502348;HSF1,2:0.217125661908;NANOG{mouse}:0.212561126276;GATA6:0.185705424925;STAT1,3:0.181699498951;RFX2..5_RFXANK_RFXAP:0.181529364036;ALX4:0.175426672194;FOX{F1,F2,J1}:0.172798725348;SOX{8,9,10}:0.156916122192;ATF5_CREB3:0.11407071491;TGIF1:0.0970735125656;ESR1:0.0885747640974;CRX:0.0790686360018;IKZF2:0.078620757849;PRRX1,2:0.0757602491704;LHX3,4:0.0731297292607;TFDP1:0.0592301017446;RXRA_VDR{dimer}:0.0524905420829;PAX2:0.0243553982515;NKX3-2:-0.00946612243698;HES1:-0.0103882197375;TP53:-0.0248525305369;CREB1:-0.0915954864285;PRDM1:-0.112168379044;bHLH_family:-0.141380649767;NKX2-3_NKX2-5:-0.145715604126;FOXQ1:-0.146672303626;EBF1:-0.152619767882;SOX5:-0.171044940095;NR1H4:-0.171457310599;PAX4:-0.202124160018;NFE2:-0.229810458963;ATF4:-0.230366473365;DBP:-0.237831449627;TLX2:-0.241852673121;MEF2{A,B,C,D}:-0.249252057959;LEF1_TCF7_TCF7L1,2:-0.278211047761;BPTF:-0.296763365785;HAND1,2:-0.304390242869;SRF:-0.334628178397;EP300:-0.390234042756;ALX1:-0.391391531104;GATA4:-0.413959866104;HOX{A5,B5}:-0.418150119657;ADNP_IRX_SIX_ZHX:-0.43834722201;HBP1_HMGB_SSRP1_UBTF:-0.442831407362;HOX{A4,D4}:-0.446136280294;NFATC1..3:-0.469194168639;FOS_FOS{B,L1}_JUN{B,D}:-0.47580072585;RXR{A,B,G}:-0.487865268285;TEF:-0.493257045261;AR:-0.505828926121;GFI1B:-0.511146385668;SOX17:-0.519680026523;NR6A1:-0.550791796542;SOX2:-0.560507912013;KLF4:-0.584431356653;FOSL2:-0.58658511533;NKX2-1,4:-0.592512316824;ONECUT1,2:-0.603083014679;BACH2:-0.606519400499;HMGA1,2:-0.618924271622;ZFP161:-0.639488788223;UFEwm:-0.640450560739;EN1,2:-0.64289009084;STAT2,4,6:-0.657564393;IKZF1:-0.682032376795;RREB1:-0.685940158176;CEBPA,B_DDIT3:-0.688195997655;NFIL3:-0.699361114087;GLI1..3:-0.734260517816;MZF1:-0.739685154939;TFAP4:-0.74098921276;SMAD1..7,9:-0.754455638358;MYBL2:-0.766991593172;STAT5{A,B}:-0.782479505782;GCM1,2:-0.784829374914;HOX{A6,A7,B6,B7}:-0.803687033526;NKX3-1:-0.818993250626;PPARG:-0.82056527378;PAX1,9:-0.826713516328;SREBF1,2:-0.836657185559;ATF2:-0.843870436334;HLF:-0.846440132248;NHLH1,2:-0.861330245316;TAL1_TCF{3,4,12}:-0.914148726196;ZNF148:-0.923810945583;MYFfamily:-0.924009766946;FOXD3:-0.928959043952;ZNF423:-0.957188083363;MTF1:-0.963145026819;EGR1..3:-0.977760003256;ZIC1..3:-0.992846577728;RFX1:-1.01291870628;XCPE1{core}:-1.03851626774;FOXO1,3,4:-1.0471811307;MTE{core}:-1.06487027425;TBP:-1.08372042353;HIC1:-1.08986749596;JUN:-1.1058763335;T:-1.12366012248;REST:-1.13330000012;NFIX:-1.14587520621;PAX5:-1.15753204538;GTF2I:-1.18459570894;NFE2L2:-1.21223264823;XBP1:-1.23331964364;NFE2L1:-1.24787716658;MAFB:-1.27537639605;MED-1{core}:-1.2857994497;FOXM1:-1.2922012403;NANOG:-1.30990483605;TFAP2{A,C}:-1.32150589921;PATZ1:-1.34822630122;TFCP2:-1.35779454385;ATF6:-1.37025780055;GTF2A1,2:-1.38000243687;HMX1:-1.388945926;GZF1:-1.43654812128;TBX4,5:-1.46044857331;MAZ:-1.47340187805;ZNF238:-1.47592322241;TLX1..3_NFIC{dimer}:-1.48167347747;ZBTB6:-1.63966328517;POU6F1:-1.67507898292;TEAD1:-1.68001545219;NR3C1:-1.68460187491;FOX{D1,D2}:-1.72871992526;SP1:-1.81297752058;TFAP2B:-1.90774420056;FOX{I1,J2}:-2.13253849766;FOXL1:-2.4673002322
}}
}}

Revision as of 14:16, 21 March 2012


Name:B lymphoblastoid cell line: GM12878 ENCODE, biol_rep3
Species:
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexfemale
ageNA
cell typeb cell
cell lineGM12878
companyNA
collaborationCarrie Davis (Cold spring Harbor Laboratories)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0



FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000826 (pro-B cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000945 (lymphocyte of B lineage)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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