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(Created page with "{{f5samples |id=FF:11716-123C6 |name=Mouse Meningeal cells, donor1 |sample_id=11716 |rna_tube_id=123C6 |rna_box=123 |rna_position=C6 |sample_cell_lot=N/A |sample_cell_...")
 
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{{f5samples
{{f5samples
|id=FF:11716-123C6
|DRA_sample_Accession=CAGE@SAMD00005064
|name=Mouse Meningeal cells, donor1
|accession_numbers=CAGE;DRX008823;DRR009695;DRZ001120;DRZ002505;DRZ012470;DRZ013855
|sample_id=11716
|ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062,UBERON:0000119,UBERON:0003210
|rna_tube_id=123C6
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000151,CL:0002320,CL:0002371,CL:0000499,CL:0000327,CL:0000255,CL:0000708
|rna_box=123
|rna_position=C6
|sample_cell_lot=N/A
|sample_cell_catalog=N/A
|sample_company=Sciencell/3H
|rna_lot_number=RNAM5762
|rna_catalog_number=custom
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_dev_stage=
|sample_tissue=meninges
|sample_donor(cell lot)=
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=meningeal cell
|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-isopropanol-v1.0
|rna_weight_ug=10.00000
|rna_concentration=0.80800
|sample_note=
|profile_hcage=CNhs12132,LSID839,release011,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000134,CL:0000144,CL:0000151,CL:0000219,CL:0000255,CL:0000327,CL:0000499,CL:0000548,CL:0000708,CL:0000723,CL:0002320,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000119,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384,UBERON:0003210
|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:0000111
 
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
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|ffid_belonging_in_development=CL:0000134
|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:11716-123C6
|is_a=EFO:0002091;;FF:0000111
|is_obsolete=
|library_id=CNhs12132
|library_id_phase_based=2:CNhs12132
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11716
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11716
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm9.nobarcode.rdna.fa.gz
|name=Mouse Meningeal cells, donor1
|namespace=FANTOM5
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12132,LSID839,release011,COMPLETED
|profile_rnaseq=
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|rna_box=123
|rna_catalog_number=custom
|rna_concentration=0.808
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=RNAM5762
|rna_od260/230=
|rna_od260/280=
|rna_position=C6
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=123C6
|rna_weight_ug=10
|sample_age=
|sample_category=primary cells
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_lot=N/A
|sample_cell_type=meningeal cell
|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=11716
|sample_note=
|sample_sex=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_tissue=meninges
|top_motifs=TP53:2.94804926256;HES1:2.33625722001;BACH2:2.07402868516;GLI1..3:1.8890883258;GTF2A1,2:1.73754514935;TFAP2{A,C}:1.6711731458;ESR1:1.33713309873;EP300:1.27871709478;GCM1,2:1.27500705093;FOS_FOS{B,L1}_JUN{B,D}:1.21273039799;TEAD1:1.10846031319;XCPE1{core}:1.0602198652;ZNF148:1.0550942057;ATF6:1.05190031054;ALX4:1.03464630425;FOSL2:1.01690248;ZIC1..3:0.975492982546;SRF:0.93743340754;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.930860941313;POU2F1..3:0.915869197341;NR1H4:0.910824306484;MTE{core}:0.87513903043;ZNF238:0.875084556471;TLX1..3_NFIC{dimer}:0.841561320314;ZNF423:0.819309066543;TAL1_TCF{3,4,12}:0.766017655406;EBF1:0.755786185636;ALX1:0.741893028538;HMX1:0.72928330584;TFCP2:0.692260456987;HAND1,2:0.615069096463;NFE2L1:0.583180359513;MAZ:0.528349810069;NFE2:0.516700626263;RXR{A,B,G}:0.516363937292;GZF1:0.480339399465;HIC1:0.475912687264;LHX3,4:0.464092277124;HSF1,2:0.443810054493;HOXA9_MEIS1:0.442774512982;UFEwm:0.429767694659;TFAP4:0.419467466434;RREB1:0.408998882479;SMAD1..7,9:0.40310053423;SP1:0.390092182199;NFE2L2:0.374686704849;MTF1:0.366889542861;PAX5:0.349714957682;PATZ1:0.343395868367;FOXP3:0.338947036829;SOX5:0.330287445791;ZNF384:0.322399914237;HOX{A5,B5}:0.317452092583;RUNX1..3:0.306228973547;NFATC1..3:0.303144820157;SPZ1:0.257981723351;TFAP2B:0.236391356856;PAX2:0.181788678202;JUN:0.159586300172;NKX2-3_NKX2-5:0.157507219066;GTF2I:0.149168184553;SOX17:0.145707812021;ATF4:0.143104695603;CDC5L:0.131160185163;EN1,2:0.116668011969;NKX3-1:0.0965802083213;HLF:0.096301272653;HBP1_HMGB_SSRP1_UBTF:0.0728492277264;PDX1:0.0727728750036;NR3C1:0.0629478831528;FOXM1:0.056212526881;IKZF1:0.0533999344834;EGR1..3:0.0511066124869;RFX1:0.038225377849;AR:0.0279801583177;ZBTB16:0.0263293904804;POU3F1..4:0.0163136958738;ONECUT1,2:0.0155042103939;KLF4:0.0073693920981;HIF1A:0.00118257996529;ADNP_IRX_SIX_ZHX:-0.00876386667743;RXRA_VDR{dimer}:-0.0106589259851;GATA4:-0.0211520758844;ELK1,4_GABP{A,B1}:-0.0482353056585;HOX{A4,D4}:-0.0485009587356;NFKB1_REL_RELA:-0.0527373561621;SREBF1,2:-0.0658031526424;NFIL3:-0.072688353544;CRX:-0.0758904289311;POU5F1:-0.0806342157074;TBP:-0.106724220958;REST:-0.135213610397;PPARG:-0.153532484608;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.16357317133;RORA:-0.172462749025;SOX2:-0.174898831664;GFI1B:-0.177733879096;PAX1,9:-0.180422921082;FOXO1,3,4:-0.185479766953;ZBTB6:-0.187857837337;LEF1_TCF7_TCF7L1,2:-0.214290470327;MYB:-0.234952997513;IRF7:-0.234960035469;NHLH1,2:-0.25095150388;MAFB:-0.263216825781;TOPORS:-0.264011381864;STAT2,4,6:-0.273831692555;TLX2:-0.281091609572;ATF2:-0.283827881137;HMGA1,2:-0.29434533403;NR5A1,2:-0.300776196972;ETS1,2:-0.301858263842;HNF4A_NR2F1,2:-0.326137655004;ELF1,2,4:-0.348554283608;CEBPA,B_DDIT3:-0.349733267831;PRRX1,2:-0.36325694713;NFY{A,B,C}:-0.363624274113;PAX8:-0.371839491234;DBP:-0.383350800342;SPIB:-0.386551306749;MYBL2:-0.397613268962;T:-0.400114342469;NANOG:-0.400240286838;NKX2-2,8:-0.411342994547;MZF1:-0.418615598202;MED-1{core}:-0.427094880768;POU1F1:-0.451129990781;STAT1,3:-0.460124361426;DMAP1_NCOR{1,2}_SMARC:-0.464184019163;TFDP1:-0.473472305276;ZFP161:-0.499571142847;YY1:-0.507364095286;FOX{D1,D2}:-0.51039803073;HNF1A:-0.541413031918;ESRRA:-0.555895071453;SPI1:-0.56691718943;FOX{F1,F2,J1}:-0.574761075381;TBX4,5:-0.577215888349;POU6F1:-0.581918148734;PAX6:-0.588391728757;MEF2{A,B,C,D}:-0.604527658208;RFX2..5_RFXANK_RFXAP:-0.623912595606;STAT5{A,B}:-0.635701051021;FOXL1:-0.65996675754;IRF1,2:-0.665690008718;AHR_ARNT_ARNT2:-0.666871036031;AIRE:-0.677264588104;NR6A1:-0.698843620775;VSX1,2:-0.699150595315;OCT4_SOX2{dimer}:-0.700058330745;E2F1..5:-0.750401152176;MYFfamily:-0.789396465566;IKZF2:-0.793174862665;BREu{core}:-0.806375189158;NRF1:-0.816753489667;FOXA2:-0.827344575947;PBX1:-0.830542072617;GATA6:-0.850629381443;CUX2:-0.869255797372;GFI1:-0.91510257901;NKX2-1,4:-0.924433487961;CDX1,2,4:-0.929316522083;PAX4:-0.929437440246;SOX{8,9,10}:-0.941342919745;PRDM1:-0.963972507113;bHLH_family:-0.973654468598;ZEB1:-1.01794685967;SNAI1..3:-1.01897523092;ZNF143:-1.090317142;NKX6-1,2:-1.10391780187;ATF5_CREB3:-1.10537608873;CREB1:-1.1187023202;EVI1:-1.11945125898;NANOG{mouse}:-1.15092151508;ARID5B:-1.18468273181;TEF:-1.19192843956;NFIX:-1.20234975061;TGIF1:-1.247724377;MYOD1:-1.27429312121;FOXN1:-1.31253241181;LMO2:-1.32581235337;PITX1..3:-1.36743769643;FOXD3:-1.37236328923;FOXQ1:-1.42195323506;RBPJ:-1.52073674819;NKX3-2:-1.5563244428;FOX{I1,J2}:-1.78795118292;FOXP1:-1.85153560481;BPTF:-2.02421726849
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11716-123C6;search_select_hide=table117:11716-123C6
}}
}}

Latest revision as of 18:16, 4 June 2020


Name:Mouse Meningeal cells, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12132
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuemeninges
dev stageNA
sexNA
ageNA
cell typemeningeal cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAM5762
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005064
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12132 CAGE DRX008823 DRR009695
Accession ID Mm9

Library idBAMCTSS
CNhs12132 DRZ001120 DRZ002505
Accession ID Mm10

Library idBAMCTSS
CNhs12132 DRZ012470 DRZ013855
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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs12132

00
10
100
1000
10000.0262
1001-0.0749
10020.0145
10030.0194
10040
10050
1006-0.0223
1007-0.352
10080
10090.115
101-0.387
10100
1011-0.108
10120
10130.0264
1014-0.0851
10150.337
10160.19
10170
10180
10190
1020
10200.481
10210.127
1022-0.124
10230
1024-0.18
1025-0.0611
10260
10270
10280
1029-0.176
1030.342
10300
10310.993
10320.0411
10330.0611
10340
10350
1036-0.00647
10370
1038-0.0736
1039-0.0747
1040
10400.545
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



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

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12132

Jaspar motifP-value
MA0002.20.0993
MA0003.10.307
MA0004.10.0965
MA0006.10.639
MA0007.10.206
MA0009.10.471
MA0014.10.326
MA0017.10.0838
MA0018.20.128
MA0019.10.737
MA0024.15.32971e-4
MA0025.10.961
MA0027.10.497
MA0028.10.545
MA0029.10.869
MA0030.10.288
MA0031.10.596
MA0035.20.101
MA0038.10.0362
MA0039.20.0884
MA0040.10.627
MA0041.10.241
MA0042.10.701
MA0043.10.34
MA0046.16.51843e-6
MA0047.20.226
MA0048.10.126
MA0050.10.0907
MA0051.10.101
MA0052.10.0681
MA0055.18.40847e-4
MA0057.10.435
MA0058.10.0489
MA0059.10.177
MA0060.10.16
MA0061.10.338
MA0062.20.0929
MA0065.20.912
MA0066.10.274
MA0067.10.539
MA0068.10.788
MA0069.10.672
MA0070.10.676
MA0071.10.757
MA0072.10.685
MA0073.10.653
MA0074.10.0703
MA0076.10.117
MA0077.10.0753
MA0078.10.085
MA0079.20.123
MA0080.20.00622
MA0081.10.275
MA0083.12.16925e-8
MA0084.10.806
MA0087.10.933
MA0088.10.664
MA0090.13.79189e-5
MA0091.10.815
MA0092.10.0461
MA0093.10.141
MA0099.21.26425e-8
MA0100.10.588
MA0101.10.694
MA0102.20.135
MA0103.10.00127
MA0104.20.471
MA0105.10.419
MA0106.12.24174e-5
MA0107.10.9
MA0108.20.206
MA0111.10.719
MA0112.20.0632
MA0113.10.532
MA0114.10.366
MA0115.10.265
MA0116.10.16
MA0117.10.377
MA0119.10.243
MA0122.10.745
MA0124.10.233
MA0125.10.74
MA0131.10.386
MA0135.10.219
MA0136.10.0435
MA0137.20.425
MA0138.20.0115
MA0139.10.771
MA0140.14.85286e-4
MA0141.10.408
MA0142.10.557
MA0143.10.411
MA0144.10.728
MA0145.10.0352
MA0146.10.00837
MA0147.10.409
MA0148.10.155
MA0149.10.313
MA0150.10.663
MA0152.10.298
MA0153.17.90682e-4
MA0154.10.199
MA0155.10.343
MA0156.11.66572e-4
MA0157.10.498
MA0159.10.771
MA0160.10.796
MA0162.10.222
MA0163.10.0402
MA0164.10.86
MA0258.10.175
MA0259.10.698



FANTOM5 phase1 novel unique motifs<b>Summary:</b>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 in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12132

Novel motifP-value
10.922
100.797
1000.764
1010.845
1020.159
1030.415
1040.656
1050.298
1060.0543
1070.923
1080.358
1090.00195
110.0152
1100.132
1110.473
1120.971
1130.381
1140.209
1150.732
1160.0146
1170.332
1180.941
1190.402
120.774
1200.602
1210.275
1220.269
1230.57
1240.0792
1250.282
1260.866
1270.169
1280.491
1290.873
130.492
1300.363
1310.559
1320.479
1330.535
1340.379
1350.407
1360.112
1370.312
1380.724
1390.435
140.453
1400.789
1410.684
1420.353
1430.0448
1440.375
1450.105
1460.876
1470.537
1480.491
1490.112
150.795
1500.227
1510.961
1520.0243
1530.255
1540.253
1550.382
1560.0201
1570.295
1580.222
1590.199
1600.935
1610.57
1620.475
1630.256
1640.836
1650.719
1660.833
1670.0195
1680.942
1690.0842
170.0613
180.371
190.168
20.261
200.508
210.0851
220.0503
230.128
240.151
250.115
260.174
270.755
280.314
290.405
30.268
300.587
310.851
320.0716
330.831
340.217
350.124
360.507
370.0577
380.206
390.497
40.25
400.0478
410.329
420.274
430.25
440.197
450.495
460.552
470.189
480.495
490.561
50.411
500.0532
510.504
520.242
530.949
540.443
550.501
560.391
570.509
580.27
590.0121
60.401
600.299
610.758
620.821
630.189
640.301
650.0271
660.364
670.596
680.737
690.0839
70.443
700.0918
710.362
720.833
730.00353
740.501
750.2
760.672
770.00887
780.684
790.907
80.269
800.259
810.387
820.973
830.542
840.52
850.0473
860.86
870.00461
880.424
890.816
90.972
900.236
910.344
920.46
930.823
940.512
950.00574
960.503
970.869
980.252
990.986



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12132


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)
0000548 (animal cell)
0000151 (secretory cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000499 (stromal cell)
0000327 (extracellular matrix secreting cell)
0000255 (eukaryotic cell)
0000708 (leptomeningeal cell)

UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0000119 (cell layer)
0003210 (blood-cerebrospinal fluid barrier)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000111 (mouse leptomeningeal cell sample)

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
CL:0000134 (mesenchymal cell)

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