FF:13283-142F7: Difference between revisions

Latest revision as of 18:55, 4 June 2020

Name:	trophoblast stem cell line R1AB differentiation
Species:	Mouse (Mus musculus)
Library ID:	CNhs13481
Sample type:	time courses
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	NA
dev stage	NA
sex	male
age	NA
cell type	SELECT CELL TYPE
cell line	NA
company	NA
collaboration	Hirohiko Kodeki(RCAI)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	R1AB +d0
catalog number	NA
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005466

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13481		CAGE		DRX008917		DRR009791

Accession ID Mm9

Library id		BAM		CTSS
CNhs13481		DRZ001216		DRZ002599

Accession ID Mm10

Library id		BAM		CTSS
CNhs13481		DRZ012566		DRZ013949

Download raw sequence, BAM & CTSS

Mm9

Fasta	BAM	CTSS
download	download	donwload

Mm10

BAM	CTSS
download	donwload

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

CNhs13481

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0749
1002	-0.0975
1003	-0.156
1004	0.0717
1005	-0.429
1006	-0.143
1007	-0.0573
1008	0
1009	-0.188
101	0.457
1010	0
1011	-0.0801
1012	0
1013	-0.145
1014	-0.0874
1015	-0.00286
1016	-0.328
1017	0
1018	0.588
1019	0
102	0
1020	0.0717
1021	0.0717
1022	0
1023	0
1024	-0.14
1025	0
1026	0
1027	-0.048
1028	0
1029	-0.0775
103	-0.0848
1030	0
1031	-0.536
1032	-0.583
1033	0.143
1034	0
1035	0
1036	0.28
1037	0
1038	-0.123
1039	-0.344
104	0
1040	-0.0865
1041	0

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed. 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 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 Analyst: Michiel de Hoon link to dataset. data

library id: CNhs13481

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.125
MA0003.1	MA0003.1	0.861
MA0004.1	MA0004.1	0.0967
MA0006.1	MA0006.1	0.989
MA0007.1	MA0007.1	0.977
MA0009.1	MA0009.1	0.285
MA0014.1	MA0014.1	0.41
MA0017.1	MA0017.1	0.674
MA0018.2	MA0018.2	0.0412
MA0019.1	MA0019.1	0.483
MA0024.1	MA0024.1	7.36205e-4
MA0025.1	MA0025.1	0.141
MA0027.1	MA0027.1	0.866
MA0028.1	MA0028.1	4.95951e-9
MA0029.1	MA0029.1	0.0281
MA0030.1	MA0030.1	0.0455
MA0031.1	MA0031.1	0.00799
MA0035.2	MA0035.2	0.126
MA0038.1	MA0038.1	0.511
MA0039.2	MA0039.2	3.11489e-4
MA0040.1	MA0040.1	0.485
MA0041.1	MA0041.1	0.355
MA0042.1	MA0042.1	0.875
MA0043.1	MA0043.1	0.0262
MA0046.1	MA0046.1	2.33362e-15
MA0047.2	MA0047.2	1.29614e-4
MA0048.1	MA0048.1	0.00571
MA0050.1	MA0050.1	4.10606e-5
MA0051.1	MA0051.1	0.0285
MA0052.1	MA0052.1	6.12687e-6
MA0055.1	MA0055.1	2.34921e-5
MA0057.1	MA0057.1	0.955
MA0058.1	MA0058.1	0.0431
MA0059.1	MA0059.1	0.00385
MA0060.1	MA0060.1	0.023
MA0061.1	MA0061.1	0.76
MA0062.2	MA0062.2	4.06262e-12
MA0065.2	MA0065.2	0.225
MA0066.1	MA0066.1	0.867
MA0067.1	MA0067.1	0.506
MA0068.1	MA0068.1	0.0526
MA0069.1	MA0069.1	0.75
MA0070.1	MA0070.1	0.329
MA0071.1	MA0071.1	0.0589
MA0072.1	MA0072.1	0.571
MA0073.1	MA0073.1	0.682
MA0074.1	MA0074.1	0.36
MA0076.1	MA0076.1	7.43519e-9
MA0077.1	MA0077.1	0.782
MA0078.1	MA0078.1	0.274
MA0079.2	MA0079.2	0.872
MA0080.2	MA0080.2	0.424
MA0081.1	MA0081.1	0.529
MA0083.1	MA0083.1	0.00537
MA0084.1	MA0084.1	0.14
MA0087.1	MA0087.1	0.744
MA0088.1	MA0088.1	0.344
MA0090.1	MA0090.1	0.889
MA0091.1	MA0091.1	0.899
MA0092.1	MA0092.1	0.172
MA0093.1	MA0093.1	0.102
MA0099.2	MA0099.2	3.52375e-5
MA0100.1	MA0100.1	0.0172
MA0101.1	MA0101.1	0.23
MA0102.2	MA0102.2	0.628
MA0103.1	MA0103.1	0.467
MA0104.2	MA0104.2	0.0346
MA0105.1	MA0105.1	0.884
MA0106.1	MA0106.1	0.0134
MA0107.1	MA0107.1	0.824
MA0108.2	MA0108.2	0.00281
MA0111.1	MA0111.1	0.521
MA0112.2	MA0112.2	0.835
MA0113.1	MA0113.1	0.723
MA0114.1	MA0114.1	0.882
MA0115.1	MA0115.1	0.00389
MA0116.1	MA0116.1	0.962
MA0117.1	MA0117.1	0.881
MA0119.1	MA0119.1	0.00762
MA0122.1	MA0122.1	0.544
MA0124.1	MA0124.1	0.484
MA0125.1	MA0125.1	0.202
MA0131.1	MA0131.1	0.0845
MA0135.1	MA0135.1	0.172
MA0136.1	MA0136.1	0.00225
MA0137.2	MA0137.2	0.0669
MA0138.2	MA0138.2	0.0021
MA0139.1	MA0139.1	0.465
MA0140.1	MA0140.1	0.0205
MA0141.1	MA0141.1	0.308
MA0142.1	MA0142.1	0.811
MA0143.1	MA0143.1	0.646
MA0144.1	MA0144.1	0.383
MA0145.1	MA0145.1	0.516
MA0146.1	MA0146.1	0.0548
MA0147.1	MA0147.1	0.0114
MA0148.1	MA0148.1	4.25595e-4
MA0149.1	MA0149.1	0.0459
MA0150.1	MA0150.1	0.212
MA0152.1	MA0152.1	0.404
MA0153.1	MA0153.1	2.15586e-7
MA0154.1	MA0154.1	0.385
MA0155.1	MA0155.1	0.568
MA0156.1	MA0156.1	3.64395e-4
MA0157.1	MA0157.1	0.00555
MA0159.1	MA0159.1	0.339
MA0160.1	MA0160.1	0.099
MA0162.1	MA0162.1	0.615
MA0163.1	MA0163.1	0.214
MA0164.1	MA0164.1	0.0223
MA0258.1	MA0258.1	0.511
MA0259.1	MA0259.1	0.0369

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 in169 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: CNhs13481

Novel motif	Logo	P-value
1	1	0.673
10	10	0.224
100	100	0.233
101	101	0.0711
102	102	0.14
103	103	0.713
104	104	0.717
105	105	0.324
106	106	0.239
107	107	0.0738
108	108	0.503
109	109	0.328
11	11	0.715
110	110	0.597
111	111	0.0892
112	112	0.878
113	113	0.298
114	114	0.803
115	115	0.363
116	116	0.512
117	117	5.62093e-4
118	118	0.34
119	119	0.372
12	12	0.613
120	120	0.478
121	121	0.923
122	122	0.254
123	123	0.0306
124	124	0.0236
125	125	0.316
126	126	0.395
127	127	0.279
128	128	0.187
129	129	0.912
13	13	0.0109
130	130	0.157
131	131	0.0157
132	132	0.241
133	133	0.0467
134	134	0.192
135	135	0.0215
136	136	0.0563
137	137	0.61
138	138	0.8
139	139	0.532
14	14	0.392
140	140	0.13
141	141	0.61
142	142	0.554
143	143	0.322
144	144	0.575
145	145	0.301
146	146	0.429
147	147	0.853
148	148	0.122
149	149	0.00528
15	15	0.632
150	150	0.665
151	151	0.136
152	152	0.122
153	153	0.75
154	154	0.699
155	155	0.0565
156	156	0.419
157	157	0.9
158	158	0.436
159	159	0.678
160	160	0.541
161	161	0.318
162	162	0.245
163	163	0.281
164	164	0.0158
165	165	0.604
166	166	0.0272
167	167	0.987
168	168	0.0645
169	169	0.7
17	17	0.786
18	18	0.499
19	19	0.31
2	2	0.0531
20	20	0.00389
21	21	0.238
22	22	0.814
23	23	0.0636
24	24	0.29
25	25	0.881
26	26	0.303
27	27	0.0459
28	28	0.752
29	29	0.00555
3	3	0.753
30	30	0.366
31	31	0.292
32	32	0.0981
33	33	0.463
34	34	0.464
35	35	0.623
36	36	0.285
37	37	0.251
38	38	0.661
39	39	0.543
4	4	0.147
40	40	0.458
41	41	0.155
42	42	0.731
43	43	0.521
44	44	0.378
45	45	0.426
46	46	0.822
47	47	0.62
48	48	0.509
49	49	0.533
5	5	0.635
50	50	0.911
51	51	0.795
52	52	0.168
53	53	0.0493
54	54	0.788
55	55	0.491
56	56	0.464
57	57	0.731
58	58	0.822
59	59	0.329
6	6	0.814
60	60	0.372
61	61	0.107
62	62	0.803
63	63	0.406
64	64	0.599
65	65	0.449
66	66	0.733
67	67	0.348
68	68	0.335
69	69	0.444
7	7	0.768
70	70	0.411
71	71	0.332
72	72	0.921
73	73	0.00652
74	74	0.334
75	75	0.0502
76	76	0.015
77	77	0.696
78	78	0.382
79	79	0.67
8	8	0.382
80	80	0.158
81	81	0.138
82	82	0.22
83	83	0.54
84	84	0.563
85	85	0.33
86	86	0.48
87	87	0.183
88	88	0.0482
89	89	0.516
9	9	0.379
90	90	0.342
91	91	0.737
92	92	0.288
93	93	0.168
94	94	0.607
95	95	0.016
96	96	0.634
97	97	0.999
98	98	0.0645
99	99	0.262

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: CNhs13481

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011194 mouse trophoblast stem cell line R1AB differentiation- day00 sample

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)
0000349 (extraembryonic cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0000351 (trophoblast cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0001062 (anatomical entity)
0000358 (blastocyst)
0000307 (blastula)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000380 (0 days sample)
0000626 (trophoblast cell line sample)
0000643 (mouse trophoblast stem cell line R1AB sample)
0000644 (trophoblast cell line differentiation sample)
0011194 (mouse trophoblast stem cell line R1AB differentiation- day00 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
NA

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005466
+|accession_numbers=CAGE;DRX008917;DRR009791;DRZ001216;DRZ002599;DRZ012566;DRZ013949
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000061,UBERON:0000465,UBERON:0002050,UBERON:0005423,UBERON:0001062,UBERON:0000358,UBERON:0000307
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0000349,CL:0000255,CL:0000034,CL:0000351
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
+|donor= biol_rep1
 |expression_enrichment_score=chr11:57645506..57645523,-!p1@Hand1!3.00!1004.80!Hand1;;chr2:103264213..103264233,+!p1@Elf5!2.60!392.77!Elf5;;chr7:147129712..147129774,+!p1@Utf1!2.34!216.12!Utf1;;chr19:5447886..5447905,+!p1@Fosl1!2.11!128.92!Fosl1;;chr9:118387300..118387317,+!p1@Eomes!2.10!123.54!Eomes;;chr8:26958093..26958148,-!p2@Ash2l!2.08!118.69!Ash2l;;chr5:148118639..148118715,-!p1@Cdx2!2.00!99.58!Cdx2;;chr2:172375081..172375105,+!p1@Tfap2c!1.99!96.89!Tfap2c;;chr12:87811081..87811100,+!p2@Esrrb!1.96!91.24!Esrrb;;chr12:87811059..87811072,+!p3@Esrrb!1.92!82.09!Esrrb;;chr2:103264245..103264268,+!p2@Elf5!1.88!75.72!Elf5;;chr7:147129777..147129814,+!p2@Utf1!1.77!57.51!Utf1;;chr9:118387969..118387984,+!p2@Eomes!1.76!55.89!Eomes;;chr8:77540128..77540145,+!p2@Hmgxb4!1.75!54.73!Hmgxb4;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.71!64.24!Zbtb11;;chr4:124334894..124334899,+!p1@Pou3f1!1.69!61.10!Pou3f1;;chr14:118636214..118636235,-!p1@Sox21!1.65!52.30!Sox21;;chr19:5447692..5447711,+!p2@Fosl1!1.63!41.45!Fosl1;;chr8:77540157..77540170,+!p3@Hmgxb4!1.62!40.28!Hmgxb4;;chr11:69468531..69468557,+!p1@Sox15!1.61!39.38!Sox15;;chr11:57645586..57645597,-!p2@Hand1!1.51!31.04!Hand1;;chr2:162880387..162880413,+!p1@Mybl2!1.49!182.48!Mybl2;;chr2:153475178..153475196,+!p1@Dnmt3b!1.49!62.44!Dnmt3b;;chr10:127095407..127095440,+!p3@Stat6!1.48!35.53!Stat6;;chr9:118387742..118387753,+!p3@Eomes!1.46!27.81!Eomes;;chr6:128250471..128250519,-!p1@Tead4!1.45!52.66!Tead4;;chr13:44825008..44825066,+!p5@Jarid2!1.42!49.07!Jarid2;;chr1:57029281..57029326,-!p1@Satb2!1.41!38.04!Satb2;;chr14:118636238..118636257,-!p2@Sox21!1.40!23.95!Sox21;;chr8:44392345..44392363,-!p1@Zfp42!1.40!23.95!Zfp42;;chr2:9800207..9800234,-!p1@Gata3!1.38!68.72!Gata3;;chr3:34548909..34548927,+!p1@Sox2!1.37!37.50!Sox2;;chrX:35180221..35180224,+!p1@Rhox6!1.36!22.07!Rhox6;;chr17:51971932..51971958,-!p2@Satb1!1.34!28.35!Satb1;;chr4:149611832..149611846,+!p3@LOC100045967,p3@LOC100503183,p4@Eno1,p4@Gm5506!1.34!20.99!Eno1;;chr2:172375136..172375149,+!p2@Tfap2c!1.34!20.72!Tfap2c;;chr6:128250380..128250442,-!p2@Tead4!1.32!24.94!Tead4;;chrX:83437105..83437121,+!p1@Nr0b1!1.31!19.56!Nr0b1;;chr17:51971960..51971979,-!p1@Satb1!1.29!24.76!Satb1;;chr4:46356509..46356527,+!p1@Foxe1!1.29!18.66!Foxe1;;chrX:103123886..103123922,-!p3@Atrx!1.27!46.38!Atrx;;chr14:122874619..122874634,+!p1@Zic2!1.27!17.58!Zic2;;chr6:128250521..128250543,-!p3@Tead4!1.26!27.27!Tead4;;chr5:148118614..148118625,-!p4@Cdx2!1.24!16.24!Cdx2;;chr7:20162663..20162678,+!p1@Zfp296!1.23!21.08!Zfp296;;chr2:103264277..103264292,+!p3@Elf5!1.22!15.70!Elf5;;chr8:94325814..94325839,-!p2@Irx3!1.21!31.76!Irx3;;chr13:72101178..72101203,-!p1@Irx1!1.21!23.42!Irx1;;chr7:147129680..147129693,+!p3@Utf1!1.21!15.25!Utf1;;chr8:44392374..44392389,-!p2@Zfp42!1.18!14.17!Zfp42;;chr6:88148650..88148669,+!p1@Gata2!1.14!107.12!Gata2;;chr8:94325321..94325366,-!p1@Irx3!1.13!30.50!Irx3;;chr2:172376528..172376543,+!p3@Tfap2c!1.12!12.29!Tfap2c;;chrX:103124643..103124660,-!p2@Atrx!1.11!79.76!Atrx;;chr10:79390075..79390115,+!p2@Arid3a!1.11!39.74!Arid3a;;chr17:51971991..51972003,-!p4@Satb1!1.11!11.93!Satb1;;chr2:162880327..162880385,+!p2@Mybl2!1.09!74.91!Mybl2;;chr9:119893782..119893802,-!p1@Csrnp1!1.08!11.12!Csrnp1;;chr2:31428221..31428244,+!p2@Fubp3!1.07!26.65!Fubp3;;chrX:58146612..58146615,-!p1@Sox3!1.07!10.77!Sox3;;chr8:94325847..94325869,-!p3@Irx3!1.06!16.78!Irx3;;chr2:153475210..153475252,+!p2@Dnmt3b!1.02!26.38!Dnmt3b;;chr11:101646566..101646603,-!p1@Etv4!1.00!29.52!Etv4;;chr12:57714257..57714278,-!p1@Nkx2-9!1.00!9.06!Nkx2-9;;chrX:133654344..133654358,-!p2@Esx1!0.98!8.52!Esx1;;chr1:57028157..57028173,-!p3@Satb2!0.98!8.52!Satb2;;chr13:53568104..53568156,-!p1@Msx2!0.97!12.65!Msx2;;chr2:162880418..162880429,+!p4@Mybl2!0.97!10.77!Mybl2;;chr11:120624132..120624143,+!p10@Hmga1,p9@Hmga1-rs1!0.97!10.59!Hmga1;;chr1:57028125..57028149,-!p2@Satb2!0.96!8.07!Satb2;;chr11:69468501..69468515,+!p2@Sox15!0.95!7.89!Sox15;;chr18:75527009..75527027,+!p1@Smad7!0.94!168.39!Smad7;;chr16:17233653..17233683,+!p1@Hic2!0.94!50.69!Hic2;;chr2:168592636..168592651,-!p1@Sall4!0.94!7.81!Sall4;;chr1:135557400..135557421,-!p4@Zbed6!0.93!7.45!Zbed6;;chr16:55966451..55966484,+!p3@Rpl24,p3@Zbtb11!0.92!45.22!Zbtb11;;chr1:135557383..135557395,-!p5@Zbed6!0.92!7.27!Zbed6;;chrX:98449898..98449913,+!p2@Foxo4!0.91!23.59!Foxo4;;chr8:94325486..94325510,-!p4@Irx3!0.91!9.42!Irx3;;chr14:122874593..122874610,+!p2@Zic2!0.91!7.18!Zic2;;chr10:119913310..119913366,-!p1@Hmga2!0.90!56.25!Hmga2;;chr4:54957910..54957954,+!p2@Zfp462!0.90!21.80!Zfp462;;chr19:5447859..5447866,+!p3@Fosl1!0.90!6.91!Fosl1;;chr11:52096804..52096896,-!p1@Tcf7!0.89!56.97!Tcf7;;chr11:101645830..101645881,-!p2@Etv4!0.88!12.56!Etv4;;chr13:72766279..72766296,+!p2@Irx2!0.88!10.05!Irx2;;chr12:57714288..57714305,-!p2@Nkx2-9!0.88!6.64!Nkx2-9;;chr1:57029076..57029098,-!p8@Satb2!0.87!6.37!Satb2;;chr6:52108291..52108323,-!p1@Hoxa1!0.87!6.37!Hoxa1;;chr4:135129538..135129558,-!p1@Grhl3!0.85!9.51!Grhl3;;chr13:72101141..72101158,-!p3@Irx1!0.85!7.81!Irx1;;chr5:77524175..77524186,-!p8@Hopx!0.85!6.10!Hopx;;chrX:133654245..133654253,-!p3@Esx1!0.85!6.01!Esx1;;chr8:26958153..26958170,-!p5@Ash2l!0.84!5.92!Ash2l;;chr13:53568191..53568219,-!p2@Msx2!0.84!5.92!Msx2;;chr17:27693622..27693635,+!p11@Hmga1-rs1,p12@Hmga1!0.83!7.45!Hmga1;;chr14:99697871..99697934,+!p1@Klf5!0.82!120.22!Klf5;;chr17:37139472..37139514,+!p1@Zfp57!0.82!40.91!Zfp57;;chr17:28409136..28409150,+!p3@Ppard!0.82!5.56!Ppard;;chr3:34548946..34548972,+!p2@Sox2!0.81!6.10!Sox2;;chr4:135129447..135129467,-!p2@Grhl3!0.80!6.55!Grhl3;;chr13:37917716..37917742,+!p9@Rreb1!0.79!9.24!Rreb1;;chr5:77524199..77524210,-!p10@Hopx!0.79!5.20!Hopx;;chr2:103264977..103264986,+!p6@Elf5!0.79!5.11!Elf5;;chr18:75527030..75527055,+!p2@Smad7!0.78!34.27!Smad7;;chr16:55966407..55966447,+!p6@Rpl24,p6@Zbtb11!0.78!13.10!Zbtb11;;chr2:162880306..162880319,+!p3@Mybl2!0.78!7.45!Mybl2;;chr13:72101161..72101177,-!p2@Irx1!0.77!7.00!Irx1;;chr6:140571128..140571148,+!p10@Aebp2!0.77!4.93!Aebp2;;chr8:44392404..44392412,-!p3@Zfp42!0.77!4.93!Zfp42;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.76!243.84!Hmga1;;chr5:77524231..77524245,-!p3@Hopx!0.76!12.56!Hopx;;chr17:48025139..48025166,-!p8@Foxp4!0.76!5.65!Foxp4;;chr14:118635860..118635885,-!p3@Sox21!0.75!4.67!Sox21;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.74!19.56!Ppp1r13l;;chr8:124806048..124806094,+!p1@Zfpm1!0.73!44.50!Zfpm1;;chr13:40829137..40829205,-!p1@Tfap2a!0.73!4.93!Tfap2a;;chr7:30906934..30907020,+!p1@Zfp382!0.72!31.67!Zfp382;;chr1:57029027..57029056,-!p7@Satb2!0.72!4.31!Satb2;;chr2:9800094..9800108,-!p3@Gata3!0.72!4.31!Gata3;;chr16:55822241..55822258,-!p1@Nfkbiz!0.71!145.43!Nfkbiz;;chr14:118636183..118636192,-!p4@Sox21!0.70!4.04!Sox21;;chr8:94325273..94325288,-!p5@Irx3!0.69!5.02!Irx3;;chr5:21290933..21291050,-!p1@Dnajc2!0.68!164.98!Dnajc2;;chr16:4594683..4594735,+!p2@Glis2!0.68!55.44!Glis2;;chr13:96095097..96095114,+!p5@Zbed3!0.68!7.18!Zbed3;;chr19:12871064..12871095,-!p2@Zfp91!0.68!3.77!Zfp91;;chr2:168780729..168780740,-!p3@LOC100502777,p3@Zfp64!0.68!3.77!Zfp64;;chr10:107769168..107769215,+!p1@Pawr!0.67!43.60!Pawr;;chr13:30077847..30077906,-!p1@E2f3!0.67!32.48!E2f3;;chr11:57645644..57645649,-!p3@Hand1!0.67!3.68!Hand1;;chr6:72739185..72739232,-!p1@Tcf7l1!0.66!42.70!Tcf7l1;;chr8:124984566..124984595,-!p1@Snai3!0.66!5.92!Snai3;;chr7:147129659..147129668,+!p4@Utf1!0.66!3.59!Utf1;;chrX:55283799..55283813,+!p1@Zic3!0.66!3.59!Zic3;;chr11:101645774..101645795,-!p9@Etv4!0.65!3.50!Etv4;;chr17:37139555..37139562,+!p6@Zfp57!0.65!3.50!Zfp57;;chr13:96095124..96095144,+!p3@Zbed3!0.64!7.36!Zbed3;;chr4:149611803..149611814,+!p6@LOC100045967,p6@LOC100503183,p7@Eno1,p8@Gm5506!0.64!3.41!Eno1;;chr9:118387933..118387942,+!p4@Eomes!0.64!3.41!Eomes;;chr2:168592591..168592604,-!p2@Sall4!0.64!3.32!Sall4;;chr5:38611720..38611799,+!p1@Lyar!0.63!103.62!Lyar;;chr6:47544966..47545046,-!p1@Ezh2!0.63!80.74!Ezh2;;chr2:167363692..167363710,+!p1@Snai1!0.63!47.28!Snai1;;chr2:163028808..163028869,+!p1@Tox2!0.63!13.55!Tox2;;chr10:107769750..107769799,+!p2@Pawr!0.63!7.89!Pawr;;chr10:80809447..80809515,-!p5@Hmg20b!0.63!4.13!Hmg20b;;chr2:103264952..103264963,+!p7@Elf5!0.63!3.23!Elf5;;chr17:86087592..86087615,-!p1@Six2!0.63!3.23!Six2;;chr17:84105510..84105540,+!p2@Mta3!0.61!19.47!Mta3;;chr6:72739034..72739055,-!p3@Tcf7l1!0.61!7.36!Tcf7l1;;chr4:54957886..54957907,+!p3@Zfp462!0.61!5.83!Zfp462;;chr12:119540395..119540415,-!p5@Sp4!0.61!5.02!Sp4;;chr2:156666727..156666753,+!p2@Tgif2!0.61!4.84!Tgif2;;chr4:61869573..61869595,-!p2@Zfp37!0.61!4.22!Zfp37;;chr8:44392310..44392319,-!p4@Zfp42!0.61!3.05!Zfp42;;chr1:57028538..57028553,-!p6@Satb2!0.61!3.05!Satb2;;chr10:80040030..80040072,-!p1@Klf16!0.60!71.95!Klf16;;chr1:137155026..137155042,-!p1@Elf3!0.60!20.81!Elf3;;chr17:84105477..84105509,+!p3@Mta3!0.60!13.64!Mta3;;chr10:5958477..5958503,+!p4@Zbtb2!0.60!5.29!Zbtb2;;chrX:7341077..7341091,+!p5@Tfe3!0.59!5.38!Tfe3;;chr13:72766250..72766273,+!p1@Irx2!0.59!4.93!Irx2;;chr8:94325446..94325459,-!p8@Irx3!0.59!3.14!Irx3;;chr3:32264565..32264613,-!p1@Zmat3!0.58!38.13!Zmat3;;chr10:127984472..127984504,-!p2@Zc3h10!0.58!10.50!Zc3h10;;chr8:13338745..13338756,+!p2@Tfdp1!0.58!7.27!Tfdp1;;chr10:119913278..119913298,-!p2@Hmga2!0.58!7.18!Hmga2;;chrX:133654667..133654672,-!p1@Esx1!0.58!2.78!Esx1;;chr2:146047829..146047847,+!p1@Insm1!0.57!5.47!Insm1;;chr9:118387565..118387569,+!p6@Eomes!0.57!2.69!Eomes;;chr9:106356211..106356242,+!p1@Pcbp4!0.56!64.32!Pcbp4;;chr8:124806017..124806040,+!p2@Zfpm1!0.56!36.06!Zfpm1;;chr7:148514080..148514108,-!p4@Deaf1!0.56!6.46!Deaf1;;chr15:76709662..76709676,+!p2@Zfp7!0.56!6.28!Zfp7;;chr17:51972017..51972022,-!p17@Satb1!0.56!2.60!Satb1;;chr6:120314480..120314487,+!p6@Kdm5a!0.56!2.60!Kdm5a;;chr12:12948633..12948651,-!p1@Mycn!0.55!30.41!Mycn;;chr2:32219200..32219213,+!p5@Ciz1!0.55!3.50!Ciz1;;chr6:64992569..64992656,+!p1@Smarcad1!0.54!93.66!Smarcad1;;chr17:28487692..28487765,-!p1@Tead3!0.54!62.53!Tead3;;chr6:72849893..72849945,-!p3@Kcmf1!0.54!16.60!Kcmf1;;chr13:30076280..30076334,-!p3@E2f3!0.54!8.79!E2f3;;chr6:38204214..38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 |fonse_cell_line=FF:0000626
@@ Line 40: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011194
 |is_obsolete=
-|name=trophoblast stem cell line R1AB differentiation, day00, biol_rep1
+|library_id=CNhs13481
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+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;13283
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520R1AB%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13481.13283-142F7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520R1AB%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13481.13283-142F7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520R1AB%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13481.13283-142F7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520R1AB%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13481.13283-142F7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520R1AB%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13481.13283-142F7.mm9.nobarcode.rdna.fa.gz
+|name=trophoblast stem cell line R1AB differentiation
 |namespace=
 |part_of=
 |profile_cagescan=,,,
 |profile_hcage=CNhs13481,LSID1024,release012,COMPLETED
-|profile_rnaseq=,,,
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@@ Line 61: / Line 76: @@
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@@ Line 79: / Line 95: @@
 |sample_strain=
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:13283-142F7;search_select_hide=table117:13283-142F7
 }}

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FF:13283-142F7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:55, 4 June 2020

CNhs13481

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	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0