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{{f5samples
 
{{f5samples
|id=FF:10235-104A1
+
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000411,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0000956,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001869,UBERON:0001890,UBERON:0001893,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0002616,UBERON:0002619,UBERON:0002780,UBERON:0002791,UBERON:0003056,UBERON:0003075,UBERON:0003080,UBERON:0004121,UBERON:0005068,UBERON:0005291,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007135,UBERON:0007284
|name=visual cortex - wildtype, neonate N15, donor1
 
|sample_id=10235
 
|rna_tube_id=104A1
 
|rna_box=104
 
|rna_position=A1
 
|sample_cell_lot=N/A
 
|sample_cell_catalog=N/A
 
|sample_company=N/A
 
|rna_lot_number=N/A
 
|rna_catalog_number=N/A
 
|sample_species=mus musculus
 
|sample_strain=
 
|sample_dev_stage=postnatal day 15
 
|sample_tissue=Visual cortex
 
|sample_donor(cell lot)=
 
|sample_sex=male
 
|sample_age=P15
 
|sample_ethnicity=N/A
 
|rna_rin=
 
|rna_od260/230=2.15
 
|rna_od260/280=2.08
 
|sample_cell_type=mixed
 
|sample_cell_line=N/A
 
|sample_collaboration=Michela Fagiolini/Alka Saxena/Piero Carninci
 
|sample_experimental_condition=age matched P15 wildtype sibling-1
 
|sample_disease=Rett Syndrome
 
|rna_sample_type=Visual cortex tissue
 
|rna_extraction_protocol=Total RNA Trizol Qiagen minElute
 
|rna_weight_ug=11.4
 
|rna_concentration=0.95
 
|sample_note=
 
|profile_hcage=CNhs13031,LSID999,release012,COMPLETED
 
|profile_cagescan=,,,
 
|profile_srnaseq=,,,
 
|profile_rnaseq=,,,
 
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000411,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0000956,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001869,UBERON:0001890,UBERON:0001893,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0002616,UBERON:0002619,UBERON:0002780,UBERON:0002791,UBERON:0003056,UBERON:0003075,UBERON:0003080,UBERON:0004121,UBERON:0005068,UBERON:0005291,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007135,UBERON:0007284
 
 
|ancestors_in_disease_facet=
 
|ancestors_in_disease_facet=
|sample_description=
+
|comment=
 +
|created_by=
 +
|creation_date=
 +
|def=
 
|fonse_cell_line=
 
|fonse_cell_line=
 
|fonse_cell_line_closure=
 
|fonse_cell_line_closure=
Line 66: Line 33:
 
|fonse_treatment=
 
|fonse_treatment=
 
|fonse_treatment_closure=
 
|fonse_treatment_closure=
|top_motifs=PAX6:3.03089933075;POU1F1:2.99109997673;EGR1..3:2.86589109227;CUX2:2.86189747146;ZFP161:2.82853555875;POU3F1..4:2.80640571662;AHR_ARNT_ARNT2:2.80400645874;REST:2.63519117917;PRRX1,2:2.54147335916;OCT4_SOX2{dimer}:2.53107007949;EVI1:2.42627341995;ZBTB6:2.42339588708;NHLH1,2:2.42149302225;PAX4:2.37294390245;MYFfamily:2.33317896877;MED-1{core}:2.33182562946;PRDM1:2.23072355965;AIRE:2.12005138401;LMO2:2.09153405339;HOXA9_MEIS1:2.04596660331;BREu{core}:2.0120470323;HMGA1,2:2.00908159108;KLF4:1.99863292249;ZBTB16:1.97634420896;UFEwm:1.94790866873;PBX1:1.90503514796;FOXQ1:1.89721815246;MTF1:1.87520037552;ATF5_CREB3:1.83882982369;ATF2:1.82467422949;JUN:1.73806103314;CREB1:1.7374271041;DBP:1.7318948561;HIC1:1.72365424753;ARID5B:1.69827465106;RREB1:1.64863319241;POU6F1:1.64416811758;MAFB:1.64245711421;RFX1:1.6231054908;TFAP2B:1.61946442134;GATA4:1.59141322715;TEF:1.58603455596;NKX6-1,2:1.5367523767;GZF1:1.53619779397;PAX5:1.47139047106;NKX2-2,8:1.44076501894;MTE{core}:1.42203290712;GFI1B:1.40901766556;TFDP1:1.39320925508;TAL1_TCF{3,4,12}:1.33194439246;ZNF384:1.32951051058;CDX1,2,4:1.31465857007;PAX8:1.30848342737;NRF1:1.29238698762;MZF1:1.24056937231;SMAD1..7,9:1.23340737619;TGIF1:1.23207580491;IKZF1:1.21477540339;HOX{A4,D4}:1.20965279798;STAT1,3:1.20913716555;ALX1:1.20851289564;GTF2I:1.19469317315;RFX2..5_RFXANK_RFXAP:1.19187235788;NANOG:1.15646420618;ZIC1..3:1.11865475577;NKX3-2:1.05741244107;CDC5L:1.02420417437;RBPJ:1.00414348744;FOXD3:0.987419366025;HAND1,2:0.967069878522;PPARG:0.929463782805;BPTF:0.921951334215;FOX{F1,F2,J1}:0.91896762143;EN1,2:0.914229836619;NFE2L2:0.908506775837;SPZ1:0.902333445043;ONECUT1,2:0.897015103105;NFIL3:0.89097060831;NKX2-3_NKX2-5:0.883837627424;SOX2:0.866282839329;bHLH_family:0.851679601394;NR3C1:0.833518023232;HOX{A5,B5}:0.804080931396;MYOD1:0.779224304309;VSX1,2:0.717099053894;HES1:0.679150209647;ZEB1:0.679011727057;TFAP2{A,C}:0.659453516931;POU5F1:0.643682385294;GLI1..3:0.630287960561;PATZ1:0.598340629489;RORA:0.598076683969;IRF7:0.54117607134;MAZ:0.519620568817;FOXN1:0.493978119933;LHX3,4:0.452687081071;NKX3-1:0.431133913448;SOX{8,9,10}:0.429441818325;HIF1A:0.40148666573;NFE2L1:0.39619446272;ATF4:0.385376946715;IKZF2:0.373693096195;FOXP1:0.367192589716;ZNF143:0.282599796233;SREBF1,2:0.255667764407;ADNP_IRX_SIX_ZHX:0.20829710177;FOXM1:0.139721230268;FOXA2:0.138496138027;NKX2-1,4:0.135779584051;NFE2:0.123092592195;FOXP3:0.0739960545819;STAT2,4,6:-0.112725607355;MEF2{A,B,C,D}:-0.133119998166;SNAI1..3:-0.226522622687;GTF2A1,2:-0.235287937508;HBP1_HMGB_SSRP1_UBTF:-0.241466987495;FOXL1:-0.281327228752;TOPORS:-0.302331399377;ESRRA:-0.315011948739;PAX2:-0.397562988332;ZNF238:-0.405024653375;HMX1:-0.455990984418;LEF1_TCF7_TCF7L1,2:-0.492085221899;MYB:-0.50066493405;MYBL2:-0.517920442719;EP300:-0.522126492059;HSF1,2:-0.522376887515;EBF1:-0.556050340824;SOX17:-0.600399784374;ZNF423:-0.605212482467;ATF6:-0.61186447384;PDX1:-0.633587214047;TFAP4:-0.641222528486;NFATC1..3:-0.657436814511;NANOG{mouse}:-0.694880051124;POU2F1..3:-0.727363155353;TLX1..3_NFIC{dimer}:-0.746632772213;YY1:-0.789667737104;ZNF148:-0.814429086311;TBX4,5:-0.815975735947;FOS_FOS{B,L1}_JUN{B,D}:-0.884094456338;ELK1,4_GABP{A,B1}:-0.896580708401;SOX5:-0.901314739468;NR6A1:-0.902687182286;HNF1A:-0.902808569983;FOSL2:-0.905981868221;GCM1,2:-0.913897446195;CEBPA,B_DDIT3:-0.915331166984;CRX:-0.920785747618;AR:-0.941799828374;SPI1:-0.953550647132;RUNX1..3:-0.996538372967;GATA6:-1.00012563173;HNF4A_NR2F1,2:-1.06544615116;T:-1.06561887118;SP1:-1.08725671653;PITX1..3:-1.09028838973;NFKB1_REL_RELA:-1.09670551887;BACH2:-1.11723474772;NR5A1,2:-1.15158758764;XCPE1{core}:-1.20289901597;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.27014416813;TFCP2:-1.30783013303;NFY{A,B,C}:-1.31129629833;NR1H4:-1.38483555954;TEAD1:-1.4169690407;GFI1:-1.43118903399;SPIB:-1.43423145401;ALX4:-1.46279623221;PAX1,9:-1.46951472569;HLF:-1.52419504316;FOX{I1,J2}:-1.52791588304;ETS1,2:-1.53180085358;IRF1,2:-1.59072362975;TBP:-1.60605508283;ELF1,2,4:-1.85866689573;DMAP1_NCOR{1,2}_SMARC:-1.85903434984;E2F1..5:-1.86312682904;TLX2:-1.88848091831;SRF:-1.98486722639;ESR1:-2.00109353834;RXRA_VDR{dimer}:-2.05024905808;FOXO1,3,4:-2.08817817602;NFIX:-2.14702792546;RXR{A,B,G}:-2.20913675648;FOX{D1,D2}:-2.2430097911;TP53:-2.26099137288;STAT5{A,B}:-2.26658557934;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-2.41497822169
 
|comment=
 
|created_by=
 
|creation_date=
 
|def=
 
 
|has_quality=
 
|has_quality=
 +
|id=FF:10235-104A1
 
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011268
 
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011268
 +
|name=visual cortex - wildtype, neonate N15, donor1
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 +
|profile_cagescan=,,,
 +
|profile_hcage=CNhs13031,LSID999,release012,COMPLETED
 +
|profile_rnaseq=,,,
 +
|profile_srnaseq=,,,
 +
|rna_box=104
 +
|rna_catalog_number=N/A
 +
|rna_concentration=0.95
 +
|rna_extraction_protocol=Total RNA Trizol Qiagen minElute
 +
|rna_lot_number=N/A
 +
|rna_od260/230=2.15
 +
|rna_od260/280=2.08
 +
|rna_position=A1
 +
|rna_rin=
 +
|rna_sample_type=Visual cortex tissue
 +
|rna_tube_id=104A1
 +
|rna_weight_ug=11.4
 +
|sample_age=P15
 +
|sample_cell_catalog=N/A
 +
|sample_cell_line=N/A
 +
|sample_cell_lot=N/A
 +
|sample_cell_type=mixed
 +
|sample_collaboration=Michela Fagiolini/Alka Saxena/Piero Carninci
 +
|sample_company=N/A
 +
|sample_description=
 +
|sample_dev_stage=postnatal day 15
 +
|sample_disease=Rett Syndrome
 +
|sample_donor(cell lot)=
 +
|sample_ethnicity=N/A
 +
|sample_experimental_condition=age matched P15 wildtype sibling-1
 +
|sample_id=10235
 +
|sample_note=
 +
|sample_sex=male
 +
|sample_species=mus musculus
 +
|sample_strain=
 +
|sample_tissue=Visual cortex
 +
|top_motifs=PAX6:3.03089933075;POU1F1:2.99109997673;EGR1..3:2.86589109227;CUX2:2.86189747146;ZFP161:2.82853555875;POU3F1..4:2.80640571662;AHR_ARNT_ARNT2:2.80400645874;REST:2.63519117917;PRRX1,2:2.54147335916;OCT4_SOX2{dimer}:2.53107007949;EVI1:2.42627341995;ZBTB6:2.42339588708;NHLH1,2:2.42149302225;PAX4:2.37294390245;MYFfamily:2.33317896877;MED-1{core}:2.33182562946;PRDM1:2.23072355965;AIRE:2.12005138401;LMO2:2.09153405339;HOXA9_MEIS1:2.04596660331;BREu{core}:2.0120470323;HMGA1,2:2.00908159108;KLF4:1.99863292249;ZBTB16:1.97634420896;UFEwm:1.94790866873;PBX1:1.90503514796;FOXQ1:1.89721815246;MTF1:1.87520037552;ATF5_CREB3:1.83882982369;ATF2:1.82467422949;JUN:1.73806103314;CREB1:1.7374271041;DBP:1.7318948561;HIC1:1.72365424753;ARID5B:1.69827465106;RREB1:1.64863319241;POU6F1:1.64416811758;MAFB:1.64245711421;RFX1:1.6231054908;TFAP2B:1.61946442134;GATA4:1.59141322715;TEF:1.58603455596;NKX6-1,2:1.5367523767;GZF1:1.53619779397;PAX5:1.47139047106;NKX2-2,8:1.44076501894;MTE{core}:1.42203290712;GFI1B:1.40901766556;TFDP1:1.39320925508;TAL1_TCF{3,4,12}:1.33194439246;ZNF384:1.32951051058;CDX1,2,4:1.31465857007;PAX8:1.30848342737;NRF1:1.29238698762;MZF1:1.24056937231;SMAD1..7,9:1.23340737619;TGIF1:1.23207580491;IKZF1:1.21477540339;HOX{A4,D4}:1.20965279798;STAT1,3:1.20913716555;ALX1:1.20851289564;GTF2I:1.19469317315;RFX2..5_RFXANK_RFXAP:1.19187235788;NANOG:1.15646420618;ZIC1..3:1.11865475577;NKX3-2:1.05741244107;CDC5L:1.02420417437;RBPJ:1.00414348744;FOXD3:0.987419366025;HAND1,2:0.967069878522;PPARG:0.929463782805;BPTF:0.921951334215;FOX{F1,F2,J1}:0.91896762143;EN1,2:0.914229836619;NFE2L2:0.908506775837;SPZ1:0.902333445043;ONECUT1,2:0.897015103105;NFIL3:0.89097060831;NKX2-3_NKX2-5:0.883837627424;SOX2:0.866282839329;bHLH_family:0.851679601394;NR3C1:0.833518023232;HOX{A5,B5}:0.804080931396;MYOD1:0.779224304309;VSX1,2:0.717099053894;HES1:0.679150209647;ZEB1:0.679011727057;TFAP2{A,C}:0.659453516931;POU5F1:0.643682385294;GLI1..3:0.630287960561;PATZ1:0.598340629489;RORA:0.598076683969;IRF7:0.54117607134;MAZ:0.519620568817;FOXN1:0.493978119933;LHX3,4:0.452687081071;NKX3-1:0.431133913448;SOX{8,9,10}:0.429441818325;HIF1A:0.40148666573;NFE2L1:0.39619446272;ATF4:0.385376946715;IKZF2:0.373693096195;FOXP1:0.367192589716;ZNF143:0.282599796233;SREBF1,2:0.255667764407;ADNP_IRX_SIX_ZHX:0.20829710177;FOXM1:0.139721230268;FOXA2:0.138496138027;NKX2-1,4:0.135779584051;NFE2:0.123092592195;FOXP3:0.0739960545819;STAT2,4,6:-0.112725607355;MEF2{A,B,C,D}:-0.133119998166;SNAI1..3:-0.226522622687;GTF2A1,2:-0.235287937508;HBP1_HMGB_SSRP1_UBTF:-0.241466987495;FOXL1:-0.281327228752;TOPORS:-0.302331399377;ESRRA:-0.315011948739;PAX2:-0.397562988332;ZNF238:-0.405024653375;HMX1:-0.455990984418;LEF1_TCF7_TCF7L1,2:-0.492085221899;MYB:-0.50066493405;MYBL2:-0.517920442719;EP300:-0.522126492059;HSF1,2:-0.522376887515;EBF1:-0.556050340824;SOX17:-0.600399784374;ZNF423:-0.605212482467;ATF6:-0.61186447384;PDX1:-0.633587214047;TFAP4:-0.641222528486;NFATC1..3:-0.657436814511;NANOG{mouse}:-0.694880051124;POU2F1..3:-0.727363155353;TLX1..3_NFIC{dimer}:-0.746632772213;YY1:-0.789667737104;ZNF148:-0.814429086311;TBX4,5:-0.815975735947;FOS_FOS{B,L1}_JUN{B,D}:-0.884094456338;ELK1,4_GABP{A,B1}:-0.896580708401;SOX5:-0.901314739468;NR6A1:-0.902687182286;HNF1A:-0.902808569983;FOSL2:-0.905981868221;GCM1,2:-0.913897446195;CEBPA,B_DDIT3:-0.915331166984;CRX:-0.920785747618;AR:-0.941799828374;SPI1:-0.953550647132;RUNX1..3:-0.996538372967;GATA6:-1.00012563173;HNF4A_NR2F1,2:-1.06544615116;T:-1.06561887118;SP1:-1.08725671653;PITX1..3:-1.09028838973;NFKB1_REL_RELA:-1.09670551887;BACH2:-1.11723474772;NR5A1,2:-1.15158758764;XCPE1{core}:-1.20289901597;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.27014416813;TFCP2:-1.30783013303;NFY{A,B,C}:-1.31129629833;NR1H4:-1.38483555954;TEAD1:-1.4169690407;GFI1:-1.43118903399;SPIB:-1.43423145401;ALX4:-1.46279623221;PAX1,9:-1.46951472569;HLF:-1.52419504316;FOX{I1,J2}:-1.52791588304;ETS1,2:-1.53180085358;IRF1,2:-1.59072362975;TBP:-1.60605508283;ELF1,2,4:-1.85866689573;DMAP1_NCOR{1,2}_SMARC:-1.85903434984;E2F1..5:-1.86312682904;TLX2:-1.88848091831;SRF:-1.98486722639;ESR1:-2.00109353834;RXRA_VDR{dimer}:-2.05024905808;FOXO1,3,4:-2.08817817602;NFIX:-2.14702792546;RXR{A,B,G}:-2.20913675648;FOX{D1,D2}:-2.2430097911;TP53:-2.26099137288;STAT5{A,B}:-2.26658557934;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-2.41497822169
 
}}
 
}}

Revision as of 05:04, 21 March 2012


Name:visual cortex - wildtype, neonate N15, donor1
Species:mus musculus
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View:
Additional information
Sample information
strainNA
tissueVisual cortex
dev stagepostnatal day 15
sexmale
ageP15
cell typemixed
cell lineN/A
companyN/A
collaborationMichela Fagiolini/Alka Saxena/Piero Carninci
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberN/A
catalog numberN/A
sample typeVisual cortex tissue
extraction protocol (Details)Total RNA Trizol Qiagen minElute



FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON: Anatomy
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000411 (visual cortex)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001890 (forebrain)
0001893 (telencephalon)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007135 (neural keel)
0007284 (presumptive neural plate)

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

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