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(Created page with "{{f5samples |id=FF:11552-120C4 |name=Mouse Astrocytes, donor2 |sample_id=11552 |rna_tube_id=120C4 |rna_box=120 |rna_position=C4 |sample_cell_lot= |sample_cell_catalog=...")
 
 
(21 intermediate revisions by the same user not shown)
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{{f5samples
 
{{f5samples
|id=FF:11552-120C4
+
|DRA_sample_Accession=CAGE@SAMD00004832
|name=Mouse Astrocytes, donor2
+
|accession_numbers=CAGE;DRX008811;DRR009683;DRZ001108;DRZ002493;DRZ012458;DRZ013843
|sample_id=11552
+
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0004121,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001017,UBERON:0001016
|rna_tube_id=120C4
+
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000095,CL:0000243,CL:0000128,CL:0000126,CL:0000125,CL:0000255,CL:0000127
|rna_box=120
 
|rna_position=C4
 
|sample_cell_lot=
 
|sample_cell_catalog=N/A
 
|sample_company=Sciencell/3H
 
|rna_lot_number=lot:3931
 
|rna_catalog_number=custom
 
|sample_species=Mouse (Mus musculus)
 
|sample_strain=
 
|sample_dev_stage=
 
|sample_tissue=brain
 
|sample_donor(cell lot)=
 
|sample_sex=
 
|sample_age=
 
|sample_ethnicity=
 
|rna_rin=9.70000
 
|rna_od260/230=
 
|rna_od260/280=
 
|sample_cell_type=astrocyte
 
|sample_cell_line=
 
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
 
|sample_experimental_condition=
 
|sample_disease=
 
|rna_sample_type=total RNA
 
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
 
|rna_weight_ug=10.00000
 
|rna_concentration=1.31000
 
|sample_note=
 
|profile_hcage=CNhs12078,LSID838,release011,COMPLETED
 
|profile_cagescan=,,,
 
|profile_srnaseq=,,,
 
|profile_rnaseq=,,,
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000030,CL:0000055,CL:0000095,CL:0000123,CL:0000125,CL:0000126,CL:0000127,CL:0000128,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000243,CL:0000255,CL:0000333,CL:0000339,CL:0000548,CL:0002319,CL:0002321,CL:0002371,CL:0002453
 
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001017,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0004121,UBERON:0005423,UBERON:0005743
 
 
|ancestors_in_disease_facet=
 
|ancestors_in_disease_facet=
|sample_description=
+
|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000105
 
+
|comment=
 +
|created_by=
 +
|creation_date=
 +
|data_phase=2
 +
|datafreeze_phase=2
 +
|def=
 +
|expression_enrichment_score=chr13:99124189..99124205,+!p1@Foxd1!2.12!195.84!Foxd1;;chr14:122874619..122874634,+!p1@Zic2!2.06!114.79!Zic2;;chr16:91270004..91270023,+!p1@Olig1!2.00!112.13!Olig1;;chr11:116196664..116196679,-!p1@Foxj1!1.88!112.55!Foxj1;;chr5:138199361..138199441,+!p2@Tsc22d4!1.81!116.61!Tsc22d4;;chr8:123640063..123640077,+!p1@Foxc2!1.56!62.57!Foxc2;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.54!42.14!Pou3f3;;chr13:31898767..31898785,+!p4@Foxc1!1.51!38.22!Foxc1;;chr9:91260594..91260612,-!p1@Zic1!1.43!25.62!Zic1;;chr2:30700881..30700916,+!p1@Prrx2!1.42!47.04!Prrx2;;chr3:34548909..34548927,+!p1@Sox2!1.42!42.42!Sox2;;chrX:90531838..90531861,+!p1@Arx!1.39!29.68!Arx;;chr10:86956396..86956411,-!p1@Ascl1!1.33!31.36!Ascl1;;chr12:74147689..74147711,-!p1@Six1!1.31!41.86!Six1;;chr3:99057269..99057306,+!p1@Tbx15!1.30!23.10!Tbx15;;chr9:91260616..91260653,-!p2@Zic1!1.30!19.04!Zic1;;chr13:31898729..31898761,+!p1@Foxc1!1.25!40.60!Foxc1;;chr8:123640090..123640101,+!p2@Foxc2!1.24!18.20!Foxc2;;chr2:38206744..38206766,+!p1@Lhx2!1.22!19.04!Lhx2;;chr16:91225808..91225824,+!p1@Olig2!1.22!15.54!Olig2;;chr5:38215819..38215823,-!p1@Msx1!1.21!39.34!Msx1;;chr13:31898637..31898653,+!p2@Foxc1!1.18!25.20!Foxc1;;chr10:84218800..84218829,+!p2@Rfx4!1.18!14.14!Rfx4;;chr10:84218895..84218909,+!p1@Rfx4!1.16!13.30!Rfx4;;chr16:91270091..91270143,+!p2@Olig1!1.12!12.04!Olig1;;chr17:86087592..86087615,-!p1@Six2!1.12!12.04!Six2;;chr12:34642510..34642530,+!p1@Twist1!1.11!37.66!Twist1;;chr16:15887371..15887385,+!p1@Cebpd!1.09!379.36!Cebpd;;chr12:34642682..34642753,+!p2@Twist1!1.09!29.82!Twist1;;chr8:87297280..87297326,-!p2@Nfix!1.08!26.32!Nfix;;chr2:30700857..30700873,+!p3@Prrx2!1.07!14.84!Prrx2;;chrX:108009761..108009788,+!p1@Pou3f4!1.07!10.78!Pou3f4;;chr4:135699731..135699747,+!p1@Id3!1.06!1170.85!Id3;;chr12:9581262..9581282,+!p1@Osr1!1.06!127.53!Osr1;;chr2:173044380..173044432,-!p1@Zbp1!1.05!24.64!Zbp1;;chr11:5761889..5761969,+!p1@Aebp1!1.04!423.32!Aebp1;;chr12:54349410..54349461,+!p1@Npas3!1.03!11.62!Npas3;;chr3:34548946..34548972,+!p2@Sox2!1.03!10.78!Sox2;;chr14:118636214..118636235,-!p1@Sox21!1.02!11.34!Sox21;;chr7:17647736..17647772,-!p1@Hif3a!1.00!32.48!Hif3a;;chr7:25292141..25292158,+!p2@Zfp428!1.00!31.92!Zfp428;;chr14:122874593..122874610,+!p2@Zic2!1.00!9.10!Zic2;;chrX:55284180..55284195,+!p2@Zic3!1.00!9.10!Zic3;;chr10:119913278..119913298,-!p2@Hmga2!0.99!20.16!Hmga2;;chr8:12395603..12395621,+!p1@Sox1!0.99!8.82!Sox1;;chr9:87626083..87626108,-!p1@Tbx18!0.98!19.04!Tbx18;;chr11:5761979..5761992,+!p2@Aebp1!0.98!17.50!Aebp1;;chr4:154010409..154010466,-!p2@Prdm16!0.94!18.62!Prdm16;;chr1:165243379..165243402,-!p3@Prrx1!0.92!11.20!Prrx1;;chr14:99698164..99698208,+!p2@Klf5!0.92!8.40!Klf5;;chr9:48644037..48644067,-!p2@Zbtb16!0.91!18.34!Zbtb16;;chr13:99124236..99124243,+!p2@Foxd1!0.90!7.00!Foxd1;;chr12:9581284..9581303,+!p2@Osr1!0.87!12.74!Osr1;;chr7:91558392..91558434,-!p1@Arnt2!0.85!17.78!Arnt2;;chr5:28492230..28492257,+!p1@En2!0.85!6.02!En2;;chr1:165243591..165243625,-!p2@Prrx1!0.84!9.38!Prrx1;;chr3:34549096..34549111,+!p3@Sox2!0.84!5.88!Sox2;;chr2:167363692..167363710,+!p1@Snai1!0.83!74.61!Snai1;;chr8:87297330..87297365,-!p5@Nfix!0.83!5.74!Nfix;;chr11:74981654..74981658,-!p1@Hic1!0.82!24.08!Hic1;;chr10:67375368..67375433,-!p1@Zfp365!0.81!10.08!Zfp365;;chr11:21901608..21901634,-!p1@Otx1!0.80!5.32!Otx1;;chr4:114581497..114581519,-!p2@Foxd2!0.80!5.32!Foxd2;;chr19:28754692..28754757,-!p1@Glis3!0.79!23.24!Glis3;;chr2:30700788..30700824,+!p2@Prrx2!0.79!8.12!Prrx2;;chr17:86020510..86020589,+!p3@Six3!0.79!5.18!Six3;;chr11:96690797..96690813,-!p1@Nfe2l1!0.78!104.29!Nfe2l1;;chrX:137077716..137077734,-!p1@Tsc22d3!0.78!38.92!Tsc22d3;;chr8:87297878..87297935,-!p3@Nfix!0.78!11.90!Nfix;;chr17:25707623..25707639,-!p1@Sox8!0.77!22.82!Sox8;;chr14:118636238..118636257,-!p2@Sox21!0.77!4.90!Sox21;;chr2:146047829..146047847,+!p1@Insm1!0.76!8.96!Insm1;;chr13:53568104..53568156,-!p1@Msx2!0.76!7.42!Msx2;;chr14:99697871..99697934,+!p1@Klf5!0.75!102.61!Klf5;;chr7:119822957..119822980,+!p2@Tead1!0.75!24.92!Tead1;;chr7:25292160..25292213,+!p3@Zfp428!0.75!12.32!Zfp428;;chr3:107398056..107398082,+!p1@Alx3!0.75!4.62!Alx3;;chr3:99057256..99057268,+!p3@Tbx15!0.75!4.62!Tbx15;;chr14:49287186..49287225,-!p1@Otx2!0.75!4.62!Otx2;;chr7:134169741..134169760,-!p10@Maz!0.74!14.70!Maz;;chr14:122874718..122874729,+!p3@Zic2!0.74!4.48!Zic2;;chr13:48356475..48356492,+!p1@Id4!0.73!106.53!Id4;;chr6:72185232..72185272,-!p1@Atoh8!0.73!13.72!Atoh8;;chr11:5761871..5761882,+!p3@Aebp1!0.73!12.46!Aebp1;;chr19:19185671..19185693,-!p1@Rorb!0.73!11.34!Rorb;;chr6:128250471..128250519,-!p1@Tead4!0.73!9.24!Tead4;;chr1:78193687..78193692,-!p1@Pax3!0.73!4.34!Pax3;;chr11:80196900..80196917,+!p3@Zfp207!0.72!15.54!Zfp207;;chr6:72185210..72185228,-!p3@Atoh8!0.72!7.70!Atoh8;;chr13:31898529..31898542,+!p5@Foxc1!0.71!5.18!Foxc1;;chr9:106356278..106356292,+!p3@Pcbp4!0.70!7.28!Pcbp4;;chr4:154010228..154010244,-!p4@Prdm16!0.70!5.74!Prdm16;;chr3:99057677..99057730,+!p2@Tbx15!0.70!4.06!Tbx15;;chr2: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076393,-!p2@Nfil3!0.10!0.98!Nfil3;;chr4:151363123..151363134,-!p2@Thap3!0.10!0.84!Thap3;;chr17:37139432..37139444,+!p4@Zfp57!0.10!0.70!Zfp57;;chr17:71200967..71200983,-!p8@Tgif1!0.10!0.56!Tgif1;;chr13:30077917..30077928,-!p4@E2f3!0.10!0.56!E2f3;;chr3:90046995..90047031,-!p2@Creb3l4!0.10!0.56!Creb3l4;;chr3:95032197..95032208,-!p3@Mllt11!0.10!0.56!Mllt11;;chr8:107793737..107793757,+!p2@Hsf4!0.10!0.42!Hsf4;;chr13:40829137..40829205,-!p1@Tfap2a!0.10!0.42!Tfap2a;;chr6:83299445..83299490,+!p1@Bola3!0.09!45.92!Bola3;;chrX:20527671..20527719,-!p1@Elk1!0.09!24.50!Elk1;;chr10:127080031..127080090,+!p1@Stat6!0.09!23.80!Stat6;;chr15:81494344..81494388,+!p1@L3mbtl2!0.09!12.46!L3mbtl2;;chr11:106134241..106134320,-!p2@Smarcd2!0.09!12.18!Smarcd2;;chr7:71083428..71083518,-!p3@Klf13!0.09!7.70!Klf13;;chr17:48061409..48061431,-!p4@Foxp4!0.09!5.04!Foxp4;;chr12:77470372..77470456,-!p1@Zbtb25!0.09!4.06!Zbtb25;;chr6:53018700..53018759,-!p2@Jazf1!0.09!3.22!Jazf1;;chr15:102034446..102034506,+!p2@Zfp740!0.09!3.08!Zfp740;;chr3:5218629..5218684,+!p1@Zfhx4!0.09!2.80!Zfhx4;;chr17:28369739..28369774,+!p2@Ppard!0.09!2.66!Ppard;;chr6:48552000..48552042,+!p@chr6:48552000..48552042,+!0.09!2.52!Zfp775;;chr4:97444280..97444291,+!p10@Nfia!0.09!1.82!Nfia;;chr6:72739034..72739055,-!p3@Tcf7l1!0.09!1.54!Tcf7l1;;chr1:64167811..64167826,-!p5@Klf7!0.09!1.54!Klf7;;chr5:104183237..104183248,+!p7@Aff1!0.09!0.98!Aff1;;chr5:125342568..125342602,+!p2@Zfp664!0.09!0.98!Zfp664;;chr10:79896129..79896163,-!p6@Tcf3!0.09!0.84!Tcf3;;chr8:118230847..118230856,-!p8@Maf!0.09!0.70!Maf;;chr7:25292310..25292329,+!p5@Zfp428!0.09!0.70!Zfp428;;chr7:135020660..135020688,+!p3@Zfp646!0.09!0.70!Zfp646;;chr7:119822940..119822945,+!p6@Tead1!0.09!0.56!Tead1;;chr17:35031524..35031539,+!p4@Zbtb12!0.09!0.56!Zbtb12;;chr15:40486427..40486437,+!p5@Zfpm2!0.09!0.56!Zfpm2;;chr14:56223387..56223401,+!p3@Irf9!0.09!0.42!Irf9;;chr8:73905967..73905978,-!p4@Nr2f6!0.09!0.42!Nr2f6;;chr4:94718879..94718898,-!p1@Jun!0.08!78.39!Jun;;chr5:125659525..125659599,-!p1@Ncor2!0.08!66.35!Ncor2;;chr7:26035739..26035757,-!p1@Erf!0.08!26.32!Erf;;chr11:102180255..102180318,-!p1@Ubtf!0.08!24.08!Ubtf;;chr7:35904304..35904320,+!p1@Cebpa!0.08!21.84!Cebpa;;chr7:134488857..134488914,-!p1@Zfp768!0.08!13.86!Zfp768;;chr11:5420954..5420969,+!p2@Xbp1!0.08!12.88!Xbp1;;chr17:34053127..34053141,+!p1@Zbtb22!0.08!11.06!Zbtb22;;chr19:5637708..5637730,+!p3@Rela!0.08!10.22!Rela;;chr17:4994904..4994953,+!p3@Arid1b!0.08!7.70!Arid1b;;chr13:55431084..55431137,-!p1@Mxd3!0.08!7.70!Mxd3;;chr8:107694742..107694823,+!p3@Cbfb!0.08!5.74!Cbfb;;chr15:25914114..25914128,+!p2@Zfp622!0.08!3.64!Zfp622;;chr8:72662966..72662991,-!p3@LOC100048268,p3@Rfxank!0.08!3.08!Rfxank;;chr19:8876976..8877011,+!p1@Zbtb3!0.08!2.80!Zbtb3;;chr4:149611311..149611317,+!p2@Eno1!0.08!2.38!Eno1;;chr12:78063146..78063159,-!p2@Max!0.08!1.96!Max;;chr4:87678673..87678706,-!p6@Mllt3!0.08!1.54!Mllt3;;chr3:135354349..135354371,-!p6@Nfkb1!0.08!1.40!Nfkb1;;chr5:104183477..104183548,+!p6@Aff1!0.08!1.26!Aff1;;chr9:48644429..48644462,-!p3@Zbtb16!0.08!1.26!Zbtb16;;chr5:65194810..65194819,+!p9@Klf3!0.08!1.26!Klf3;;chr3:54611738..54611749,-!p3@Rfxap!0.08!1.12!Rfxap;;chr8:87237732..87237745,-!p7@Nfix!0.08!0.84!Nfix;;chr5:125659510..125659517,-!p3@Ncor2!0.08!0.70!Ncor2;;chr11:87881881..87881887,+!p5@Vezf1!0.08!0.70!Vezf1;;chr11:120494908..120494919,-!p4@Mafg!0.08!0.70!Mafg;;chr5:120120981..120120992,+!p5@Tbx3!0.08!0.56!Tbx3;;chr4:151235871..151235882,-!p7@Camta1!0.08!0.56!Camta1;;chr5:107003725..107003746,-!p5@Zfp644!0.08!0.56!Zfp644;;chr7:20162663..20162678,+!p1@Zfp296!0.08!0.56!Zfp296;;chr7:5003087..5003098,+!p6@Zfp580!0.08!0.42!Zfp580;;chr9:63869705..63869713,-!p8@Smad6!0.08!0.42!Smad6;;
 +
|ffid_belonging_in_development=CL:0000133,CL:0000339,CL:0000221
 
|fonse_cell_line=
 
|fonse_cell_line=
 
|fonse_cell_line_closure=
 
|fonse_cell_line_closure=
Line 67: Line 40:
 
|fonse_treatment=
 
|fonse_treatment=
 
|fonse_treatment_closure=
 
|fonse_treatment_closure=
 +
|has_quality=
 +
|id=FF:11552-120C4
 +
|is_a=EFO:0002091;;FF:0000105
 +
|is_obsolete=
 +
|library_id=CNhs12078
 +
|library_id_phase_based=2:CNhs12078
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11552
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11552
 +
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%252c%2520donor2.CNhs12078.11552-120C4.mm10.nobarcode.bam
 +
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%252c%2520donor2.CNhs12078.11552-120C4.mm10.nobarcode.ctss.bed.gz
 +
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%252c%2520donor2.CNhs12078.11552-120C4.mm9.nobarcode.bam
 +
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%252c%2520donor2.CNhs12078.11552-120C4.mm9.ctss.bed.gz
 +
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%252c%2520donor2.CNhs12078.11552-120C4.mm9.nobarcode.rdna.fa.gz
 +
|name=Mouse Astrocytes, donor2
 +
|namespace=FANTOM5
 +
|part_of=
 +
|profile_cagescan=,,,
 +
|profile_hcage=CNhs12078,LSID838,release011,COMPLETED
 +
|profile_rnaseq=
 +
|profile_srnaseq=,,,
 +
|repeat_enrich_byfamily=-0.0893457570968351,0,0,0,0,0,-0.6239816537174,0,0,0,0,-0.0274395619094528,0,0,0,0,0.0284498392435444,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.311478974606717,-0.451222036856999,0,0,0,0,0,-0.209322725495826,-0.00257065767513376,-0.22227340720995,-0.533989443821847,-0.11759275228454,0.296644341734729,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0.0236221220205411,0,0,-0.0276268839918301,-0.214775938950726,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,-0.0398282379913335,0.00591131580555515,0,0,0,-0.0512319033244535,0.599945331254664,-0.0788315948399074,0,0,0,0,0,0,0.264591905432095,0.0214695456629341,0.213080815224162,0,0,0.0568996784870888,0.24036414809762,0
 +
|rna_box=120
 +
|rna_catalog_number=custom
 +
|rna_concentration=1.31
 +
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
 +
|rna_lot_number=lot:3931
 +
|rna_od260/230=
 +
|rna_od260/280=
 +
|rna_position=C4
 +
|rna_rin=9.7
 +
|rna_sample_type=total RNA
 +
|rna_tube_id=120C4
 +
|rna_weight_ug=10
 +
|sample_age=
 +
|sample_category=primary cells
 +
|sample_cell_catalog=N/A
 +
|sample_cell_line=
 +
|sample_cell_lot=
 +
|sample_cell_type=astrocyte
 +
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
 +
|sample_company=Sciencell/3H
 +
|sample_description=
 +
|sample_dev_stage=
 +
|sample_disease=
 +
|sample_donor(cell lot)=
 +
|sample_ethnicity=
 +
|sample_experimental_condition=
 +
|sample_id=11552
 +
|sample_note=
 +
|sample_sex=
 +
|sample_species=Mouse (Mus musculus)
 +
|sample_strain=
 +
|sample_tissue=brain
 +
|top_motifs=AR:2.22708754621;HES1:2.13765409887;BACH2:2.09173360842;TP53:1.85423096225;GLI1..3:1.53957020388;GCM1,2:1.41934542423;EP300:1.40604342685;GTF2A1,2:1.39589060882;ZNF423:1.35363116247;NFE2L1:1.31412797803;TFAP2{A,C}:1.29809329131;TLX1..3_NFIC{dimer}:1.23535370024;ZNF148:1.21499012424;XCPE1{core}:1.17597244262;NFE2L2:1.16642245305;TFCP2:1.16102755196;ESR1:1.13860697273;TFAP4:1.13792521337;UFEwm:1.09684729289;TEAD1:1.04354064848;ATF6:0.942586759476;HMX1:0.927705420326;EBF1:0.921431532667;HOXA9_MEIS1:0.921258191843;RFX1:0.916777727858;MTF1:0.865946927211;RXR{A,B,G}:0.848864499085;IKZF1:0.820762513103;POU2F1..3:0.767757970288;FOSL2:0.744248786725;PAX5:0.724243675363;ZIC1..3:0.710079831651;ALX4:0.693937445086;SP1:0.67285890212;FOXP3:0.661885270657;MTE{core}:0.655713890136;NR1H4:0.615163942641;FOS_FOS{B,L1}_JUN{B,D}:0.614971800681;SMAD1..7,9:0.577572952776;MAZ:0.574324302869;ZNF238:0.535803301663;VSX1,2:0.508291825945;HIC1:0.506367394016;HOX{A5,B5}:0.493583555033;PATZ1:0.472245820091;GTF2I:0.448734974599;TOPORS:0.424656837468;KLF4:0.339399959276;T:0.337723364652;NKX3-1:0.336918078259;RXRA_VDR{dimer}:0.309199779025;REST:0.295688904788;TBX4,5:0.295337122186;NFY{A,B,C}:0.2949174359;NFATC1..3:0.289132061453;PAX2:0.28130993391;RREB1:0.281155890097;ONECUT1,2:0.268406685431;HBP1_HMGB_SSRP1_UBTF:0.249548208099;TFDP1:0.246142680404;LEF1_TCF7_TCF7L1,2:0.234968022877;HSF1,2:0.213318767849;STAT2,4,6:0.206134978505;ZBTB6:0.202544893075;NKX2-3_NKX2-5:0.188790483949;NFE2:0.174521212387;RFX2..5_RFXANK_RFXAP:0.17158748653;TFAP2B:0.168907603665;HLF:0.158430991092;GZF1:0.134040136227;ZNF384:0.119573142205;NFIL3:0.113565781861;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0611451326933;POU5F1:0.0434128794399;FOX{F1,F2,J1}:0.03310824833;HAND1,2:0.0319963273004;STAT5{A,B}:-0.0110644012306;IRF7:-0.0112395590121;MYBL2:-0.0159943013205;GATA4:-0.0233127524201;STAT1,3:-0.0308988482646;FOXO1,3,4:-0.0459992096938;GFI1B:-0.0601998638895;RUNX1..3:-0.070001489066;SOX2:-0.0799373434585;SPZ1:-0.0842453089541;IRF1,2:-0.098460879665;NFKB1_REL_RELA:-0.119092638324;OCT4_SOX2{dimer}:-0.131990040225;MYOD1:-0.137996248743;MYB:-0.139833822907;JUN:-0.146705215045;ZFP161:-0.159956848322;NR5A1,2:-0.162809139212;POU3F1..4:-0.171613861715;HMGA1,2:-0.172602490865;SOX17:-0.192030705723;GFI1:-0.193361755769;ATF4:-0.195189298035;FOXN1:-0.201384509655;MED-1{core}:-0.208242381541;HOX{A4,D4}:-0.222552742686;NKX2-2,8:-0.247521303574;MYFfamily:-0.247859142219;MZF1:-0.253750449454;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.255721360719;TBP:-0.257452059682;PAX1,9:-0.26472509147;FOX{D1,D2}:-0.269532213778;FOXL1:-0.284364682062;FOXM1:-0.2900326936;HNF4A_NR2F1,2:-0.306347523915;RORA:-0.308955990398;EGR1..3:-0.310628846845;PDX1:-0.314937327025;MAFB:-0.321494584004;BREu{core}:-0.32292086157;EN1,2:-0.327279246286;ESRRA:-0.327593545934;SRF:-0.33068109123;CRX:-0.338854247279;SREBF1,2:-0.347331909777;SOX{8,9,10}:-0.367645814058;CEBPA,B_DDIT3:-0.369364215488;ARID5B:-0.388605039921;ADNP_IRX_SIX_ZHX:-0.400905290546;PRRX1,2:-0.434060534593;ZEB1:-0.446125676576;NKX3-2:-0.462315562601;LHX3,4:-0.488912236961;ELF1,2,4:-0.511243253406;NFIX:-0.514161100096;NHLH1,2:-0.515313260849;LMO2:-0.515619828689;TAL1_TCF{3,4,12}:-0.524489416695;CDC5L:-0.536607733331;DBP:-0.538811884601;ETS1,2:-0.551753233228;ELK1,4_GABP{A,B1}:-0.55376744315;SPIB:-0.569335247192;bHLH_family:-0.572787170361;MEF2{A,B,C,D}:-0.574546057576;PRDM1:-0.575292739696;HNF1A:-0.579214942106;PAX8:-0.579766667484;HIF1A:-0.626951038618;NR3C1:-0.629775300931;NKX2-1,4:-0.641242017046;RBPJ:-0.644227634832;POU6F1:-0.64898756797;SOX5:-0.686043165796;NANOG:-0.695974327317;E2F1..5:-0.703603886591;SPI1:-0.727927197482;DMAP1_NCOR{1,2}_SMARC:-0.762387039419;TLX2:-0.768710421449;ATF2:-0.772166702102;ZBTB16:-0.777121143534;IKZF2:-0.777477307763;FOXA2:-0.803180980526;NRF1:-0.825533405215;SNAI1..3:-0.847621706262;PPARG:-0.861894952115;NKX6-1,2:-0.872139095321;ALX1:-0.89027023199;NANOG{mouse}:-0.947792523713;PAX6:-0.951592365921;FOXD3:-0.961027229949;YY1:-0.986545846766;PAX4:-1.00179132629;POU1F1:-1.00553712871;CREB1:-1.01199672688;TGIF1:-1.04237987091;ZNF143:-1.07473106324;CUX2:-1.08031341151;NR6A1:-1.08093214834;GATA6:-1.11775993695;AIRE:-1.16705693303;AHR_ARNT_ARNT2:-1.17817804514;ATF5_CREB3:-1.24803424241;PBX1:-1.32456712013;EVI1:-1.35021570907;PITX1..3:-1.35268079189;FOX{I1,J2}:-1.45212223432;TEF:-1.46353878958;FOXQ1:-1.66891947896;FOXP1:-1.67901362551;BPTF:-1.68076408515;CDX1,2,4:-1.9380658011
 +
|xref=
 
}}
 
}}

Latest revision as of 11:49, 10 August 2017


Name:Mouse Astrocytes, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12078
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexNA
ageNA
cell typeastrocyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:3931
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004832
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12078 CAGE DRX008811 DRR009683
Accession ID Mm9

Library idBAMCTSS
CNhs12078 DRZ001108 DRZ002493
Accession ID Mm10

Library idBAMCTSS
CNhs12078 DRZ012458 DRZ013843
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data

CNhs12078

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.354
1001 --0.0465
1002 0.0991
1003 0.233
1004 0.13
1005 --0.0389
1006 --0.0355
1007 --0.259
1008 0
1009 0.19
101 --0.316
1010 0
1011 --0.115
1012 0
1013 0.163
1014 0.0569
1015 0.102
1016 0.207
1017 0
1018 0
1019 0
102 0
1020 0.563
1021 0.193
1022 --0.0487
1023 0
1024 0
1025 0
1026 0
1027 0.152
1028 0
1029 --0.176
103 0.322
1030 0
1031 0.923
1032 0.392
1033 --0.0183
1034 0
1035 0
1036 --0.125
1037 0
1038 0.0445
1039 --0.0332
104 0
1040 0.464
1041 0



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs12078

Jaspar motif P-value
MA0002.2 0.821
MA0003.1 0.295
MA0004.1 0.744
MA0006.1 0.337
MA0007.1 0.0272
MA0009.1 0.359
MA0014.1 0.577
MA0017.1 0.00361
MA0018.2 0.0138
MA0019.1 0.787
MA0024.1 0.00658
MA0025.1 0.454
MA0027.1 0.77
MA0028.1 0.0205
MA0029.1 0.994
MA0030.1 0.593
MA0031.1 0.726
MA0035.2 0.00238
MA0038.1 0.315
MA0039.2 0.0449
MA0040.1 0.261
MA0041.1 0.213
MA0042.1 0.544
MA0043.1 0.425
MA0046.1 5.59394e-7
MA0047.2 0.325
MA0048.1 0.367
MA0050.1 0.852
MA0051.1 0.883
MA0052.1 0.0234
MA0055.1 0.056
MA0057.1 0.362
MA0058.1 0.724
MA0059.1 0.623
MA0060.1 0.295
MA0061.1 0.814
MA0062.2 5.5672e-6
MA0065.2 0.683
MA0066.1 0.945
MA0067.1 0.383
MA0068.1 0.495
MA0069.1 0.329
MA0070.1 0.722
MA0071.1 0.322
MA0072.1 0.522
MA0073.1 0.769
MA0074.1 0.319
MA0076.1 0.00365
MA0077.1 0.0785
MA0078.1 0.813
MA0079.2 0.0231
MA0080.2 3.95316e-5
MA0081.1 0.0547
MA0083.1 0.341
MA0084.1 0.58
MA0087.1 0.741
MA0088.1 0.667
MA0090.1 0.00108
MA0091.1 0.312
MA0092.1 0.631
MA0093.1 0.866
MA0099.2 2.24565e-5
MA0100.1 0.771
MA0101.1 0.472
MA0102.2 0.0331
MA0103.1 0.00296
MA0104.2 0.749
MA0105.1 0.997
MA0106.1 0.0322
MA0107.1 0.207
MA0108.2 0.767
MA0111.1 0.679
MA0112.2 0.257
MA0113.1 0.177
MA0114.1 0.0332
MA0115.1 0.122
MA0116.1 0.587
MA0117.1 0.395
MA0119.1 0.335
MA0122.1 0.87
MA0124.1 0.608
MA0125.1 0.772
MA0131.1 0.108
MA0135.1 0.313
MA0136.1 1.03871e-6
MA0137.2 0.971
MA0138.2 0.199
MA0139.1 0.637
MA0140.1 1.81004e-6
MA0141.1 0.907
MA0142.1 0.913
MA0143.1 0.393
MA0144.1 0.784
MA0145.1 0.05
MA0146.1 0.029
MA0147.1 0.73
MA0148.1 0.15
MA0149.1 0.795
MA0150.1 0.676
MA0152.1 0.427
MA0153.1 5.13161e-5
MA0154.1 0.34
MA0155.1 0.316
MA0156.1 1.25835e-9
MA0157.1 0.592
MA0159.1 0.645
MA0160.1 0.588
MA0162.1 0.111
MA0163.1 0.324
MA0164.1 0.889
MA0258.1 0.905
MA0259.1 0.472



FANTOM5 phase1 novel unique motifsSummary:Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs12078

Novel motif P-value
1 0.424
10 0.646
100 0.666
101 0.845
102 0.367
103 0.272
104 0.783
105 0.457
106 0.0804
107 0.46
108 0.628
109 0.00725
11 0.209
110 0.433
111 0.36
112 0.42
113 0.305
114 0.895
115 0.936
116 0.0517
117 0.691
118 0.452
119 0.885
12 0.636
120 0.663
121 0.232
122 0.184
123 0.83
124 0.702
125 0.918
126 0.213
127 0.635
128 0.363
129 0.423
13 0.89
130 0.508
131 0.91
132 0.225
133 0.422
134 0.39
135 0.546
136 0.0109
137 0.305
138 0.835
139 0.146
14 0.722
140 0.073
141 0.638
142 0.159
143 0.117
144 0.978
145 0.989
146 0.863
147 0.357
148 0.622
149 0.146
15 0.759
150 0.231
151 0.845
152 0.0263
153 0.132
154 0.203
155 0.247
156 0.00168
157 0.547
158 0.0256
159 0.0359
160 0.884
161 0.512
162 0.616
163 0.211
164 0.0154
165 0.915
166 0.337
167 0.0293
168 0.738
169 0.148
17 0.34
18 0.527
19 0.195
2 0.0133
20 0.831
21 0.271
22 0.086
23 0.0563
24 0.105
25 0.122
26 0.91
27 0.487
28 0.403
29 0.716
3 0.875
30 0.0987
31 0.773
32 0.0558
33 0.762
34 0.0839
35 0.164
36 0.0581
37 0.149
38 0.467
39 0.175
4 0.737
40 0.909
41 0.909
42 0.966
43 0.556
44 0.308
45 0.238
46 0.532
47 0.593
48 0.986
49 0.107
5 0.0909
50 0.0946
51 0.559
52 0.0985
53 0.741
54 0.287
55 0.337
56 0.669
57 0.451
58 0.0695
59 0.0211
6 0.676
60 0.17
61 0.911
62 0.344
63 0.13
64 0.467
65 0.0336
66 0.461
67 0.972
68 0.424
69 0.175
7 0.364
70 0.88
71 0.733
72 0.67
73 0.00548
74 0.625
75 0.965
76 0.226
77 0.0081
78 0.0398
79 0.822
8 0.59
80 0.0955
81 0.33
82 0.966
83 0.932
84 0.288
85 0.0445
86 0.958
87 0.00104
88 0.541
89 0.879
9 0.999
90 0.648
91 0.989
92 0.583
93 0.104
94 0.197
95 0.00122
96 0.155
97 0.584
98 0.119
99 0.159



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs12078


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000128 (oligodendrocyte)
0000126 (macroglial cell)
0000125 (glial cell)
0000255 (eukaryotic cell)
0000127 (astrocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000105 (mouse astrocyte sample)

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

link to source data
data

CL:0000133 (neurectodermal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)