FF:13290-142G5: Difference between revisions

Latest revision as of 18:55, 4 June 2020

Name:	trophoblast stem cell line Rybp differentiation
Species:	Mouse (Mus musculus)
Library ID:	CNhs13519
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	Rybp +d0
catalog number	NA
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004700

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13519		CAGE		DRX008918		DRR009792

Accession ID Mm9

Library id		BAM		CTSS
CNhs13519		DRZ001217		DRZ002600

Accession ID Mm10

Library id		BAM		CTSS
CNhs13519		DRZ012567		DRZ013950

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

CNhs13519

0	0
1	0
10	0
100	0
1000	-0.00178
1001	-0.0631
1002	-0.0941
1003	-0.175
1004	0
1005	-0.111
1006	-0.248
1007	-0.124
1008	0
1009	-0.19
101	0.318
1010	0
1011	-0.0725
1012	0
1013	-0.115
1014	-0.0874
1015	-0.063
1016	-0.327
1017	0
1018	0.793
1019	0
102	0
1020	0.177
1021	0.077
1022	-0.124
1023	0
1024	-0.14
1025	0
1026	0
1027	-0.048
1028	0
1029	-0.0989
103	-0.0861
1030	0
1031	-0.521
1032	-0.458
1033	0.0595
1034	0
1035	0
1036	-0.0321
1037	0
1038	-0.0973
1039	-0.281
104	0
1040	-0.0535
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: CNhs13519

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.21
MA0003.1	MA0003.1	0.738
MA0004.1	MA0004.1	0.239
MA0006.1	MA0006.1	0.987
MA0007.1	MA0007.1	0.869
MA0009.1	MA0009.1	0.336
MA0014.1	MA0014.1	0.0949
MA0017.1	MA0017.1	0.761
MA0018.2	MA0018.2	0.00107
MA0019.1	MA0019.1	0.525
MA0024.1	MA0024.1	0.00164
MA0025.1	MA0025.1	0.347
MA0027.1	MA0027.1	0.843
MA0028.1	MA0028.1	9.22102e-8
MA0029.1	MA0029.1	2.56211e-4
MA0030.1	MA0030.1	0.268
MA0031.1	MA0031.1	0.0398
MA0035.2	MA0035.2	0.173
MA0038.1	MA0038.1	0.851
MA0039.2	MA0039.2	3.27972e-6
MA0040.1	MA0040.1	0.904
MA0041.1	MA0041.1	0.185
MA0042.1	MA0042.1	0.613
MA0043.1	MA0043.1	0.00613
MA0046.1	MA0046.1	1.78922e-12
MA0047.2	MA0047.2	0.00571
MA0048.1	MA0048.1	0.0248
MA0050.1	MA0050.1	5.59512e-5
MA0051.1	MA0051.1	0.0799
MA0052.1	MA0052.1	2.43036e-5
MA0055.1	MA0055.1	6.18729e-6
MA0057.1	MA0057.1	0.525
MA0058.1	MA0058.1	0.119
MA0059.1	MA0059.1	0.0358
MA0060.1	MA0060.1	0.00204
MA0061.1	MA0061.1	0.826
MA0062.2	MA0062.2	1.13817e-10
MA0065.2	MA0065.2	0.31
MA0066.1	MA0066.1	0.837
MA0067.1	MA0067.1	0.248
MA0068.1	MA0068.1	0.00301
MA0069.1	MA0069.1	0.857
MA0070.1	MA0070.1	0.53
MA0071.1	MA0071.1	0.0803
MA0072.1	MA0072.1	0.329
MA0073.1	MA0073.1	0.575
MA0074.1	MA0074.1	0.414
MA0076.1	MA0076.1	3.85008e-7
MA0077.1	MA0077.1	0.796
MA0078.1	MA0078.1	0.235
MA0079.2	MA0079.2	0.192
MA0080.2	MA0080.2	0.378
MA0081.1	MA0081.1	0.862
MA0083.1	MA0083.1	0.0261
MA0084.1	MA0084.1	0.598
MA0087.1	MA0087.1	0.554
MA0088.1	MA0088.1	0.155
MA0090.1	MA0090.1	0.407
MA0091.1	MA0091.1	0.778
MA0092.1	MA0092.1	0.541
MA0093.1	MA0093.1	0.217
MA0099.2	MA0099.2	2.86627e-9
MA0100.1	MA0100.1	0.0307
MA0101.1	MA0101.1	0.215
MA0102.2	MA0102.2	0.759
MA0103.1	MA0103.1	0.0804
MA0104.2	MA0104.2	0.081
MA0105.1	MA0105.1	0.446
MA0106.1	MA0106.1	0.00284
MA0107.1	MA0107.1	0.688
MA0108.2	MA0108.2	0.172
MA0111.1	MA0111.1	0.394
MA0112.2	MA0112.2	0.745
MA0113.1	MA0113.1	0.425
MA0114.1	MA0114.1	0.961
MA0115.1	MA0115.1	0.00624
MA0116.1	MA0116.1	0.654
MA0117.1	MA0117.1	0.871
MA0119.1	MA0119.1	0.00133
MA0122.1	MA0122.1	0.581
MA0124.1	MA0124.1	0.382
MA0125.1	MA0125.1	0.663
MA0131.1	MA0131.1	0.0609
MA0135.1	MA0135.1	0.798
MA0136.1	MA0136.1	0.0198
MA0137.2	MA0137.2	0.0197
MA0138.2	MA0138.2	0.00707
MA0139.1	MA0139.1	0.273
MA0140.1	MA0140.1	0.0237
MA0141.1	MA0141.1	0.891
MA0142.1	MA0142.1	0.694
MA0143.1	MA0143.1	0.835
MA0144.1	MA0144.1	0.174
MA0145.1	MA0145.1	0.784
MA0146.1	MA0146.1	0.00548
MA0147.1	MA0147.1	0.0386
MA0148.1	MA0148.1	0.00651
MA0149.1	MA0149.1	0.0368
MA0150.1	MA0150.1	0.231
MA0152.1	MA0152.1	0.0555
MA0153.1	MA0153.1	4.59169e-6
MA0154.1	MA0154.1	0.456
MA0155.1	MA0155.1	0.443
MA0156.1	MA0156.1	0.0111
MA0157.1	MA0157.1	0.049
MA0159.1	MA0159.1	0.361
MA0160.1	MA0160.1	0.157
MA0162.1	MA0162.1	0.691
MA0163.1	MA0163.1	0.977
MA0164.1	MA0164.1	0.0215
MA0258.1	MA0258.1	0.75
MA0259.1	MA0259.1	0.043

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: CNhs13519

Novel motif	Logo	P-value
1	1	0.418
10	10	0.409
100	100	0.427
101	101	0.0394
102	102	0.0654
103	103	0.942
104	104	0.705
105	105	0.303
106	106	0.257
107	107	0.0809
108	108	0.826
109	109	0.453
11	11	0.913
110	110	0.845
111	111	0.0434
112	112	0.863
113	113	0.566
114	114	0.901
115	115	0.587
116	116	0.794
117	117	2.98606e-4
118	118	0.346
119	119	0.653
12	12	0.596
120	120	0.746
121	121	0.769
122	122	0.396
123	123	0.0115
124	124	0.0796
125	125	0.777
126	126	0.441
127	127	0.338
128	128	0.136
129	129	0.689
13	13	0.00622
130	130	0.0677
131	131	0.00449
132	132	0.196
133	133	0.0429
134	134	0.256
135	135	0.00932
136	136	0.019
137	137	0.565
138	138	0.54
139	139	0.706
14	14	0.396
140	140	0.316
141	141	0.91
142	142	0.729
143	143	0.294
144	144	0.697
145	145	0.585
146	146	0.533
147	147	0.923
148	148	0.0349
149	149	0.0517
15	15	0.379
150	150	0.637
151	151	0.174
152	152	0.0503
153	153	0.909
154	154	0.855
155	155	0.0513
156	156	0.00987
157	157	0.538
158	158	0.456
159	159	0.891
160	160	0.583
161	161	0.0905
162	162	0.32
163	163	0.192
164	164	0.0193
165	165	0.742
166	166	0.0224
167	167	0.865
168	168	0.0764
169	169	0.34
17	17	0.957
18	18	0.422
19	19	0.478
2	2	0.161
20	20	0.00903
21	21	0.385
22	22	0.84
23	23	0.118
24	24	0.215
25	25	0.951
26	26	0.573
27	27	0.0308
28	28	0.837
29	29	0.00671
3	3	0.746
30	30	0.495
31	31	0.238
32	32	0.0297
33	33	0.722
34	34	0.697
35	35	0.242
36	36	0.575
37	37	0.268
38	38	0.88
39	39	0.785
4	4	0.0966
40	40	0.437
41	41	0.171
42	42	0.708
43	43	0.368
44	44	0.222
45	45	0.531
46	46	0.953
47	47	0.649
48	48	0.754
49	49	0.448
5	5	0.306
50	50	0.685
51	51	0.605
52	52	0.258
53	53	0.0572
54	54	0.816
55	55	0.335
56	56	0.589
57	57	0.752
58	58	0.966
59	59	0.278
6	6	0.611
60	60	0.573
61	61	0.136
62	62	0.881
63	63	0.339
64	64	0.389
65	65	0.533
66	66	0.534
67	67	0.3
68	68	0.358
69	69	0.265
7	7	0.802
70	70	0.369
71	71	0.696
72	72	0.88
73	73	0.0078
74	74	0.211
75	75	0.0462
76	76	0.0256
77	77	0.766
78	78	0.242
79	79	0.851
8	8	0.663
80	80	0.308
81	81	0.224
82	82	0.424
83	83	0.722
84	84	0.376
85	85	0.455
86	86	0.553
87	87	0.0497
88	88	0.0234
89	89	0.763
9	9	0.437
90	90	0.704
91	91	0.433
92	92	0.497
93	93	0.101
94	94	0.322
95	95	0.0128
96	96	0.845
97	97	0.908
98	98	0.0171
99	99	0.184

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: CNhs13519

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011201 mouse trophoblast stem cell line Rybp 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)
0000644 (trophoblast cell line differentiation sample)
0000642 (mouse trophoblast stem cell line Rybp sample)
0011201 (mouse trophoblast stem cell line Rybp 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@SAMD00004700
+|accession_numbers=CAGE;DRX008918;DRR009792;DRZ001217;DRZ002600;DRZ012567;DRZ013950
 |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:0000144,CL:0000548,CL:0000034,CL:0000012,CL:0002371,CL:0000004,CL:0000349,CL:0000255,CL:0000351
+|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0000349,CL:0000255,CL:0000034,CL:0000351
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000101,FF:0000103,FF:0000001,FF:0000350,FF:0000380,FF:0000626,FF:0000644,FF:0000642,FF:0011201
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
+|donor= biol_rep1
 |expression_enrichment_score=chr11:57645506..57645523,-!p1@Hand1!2.97!930.08!Hand1;;chr7:147129712..147129774,+!p1@Utf1!2.25!175.27!Utf1;;chr2:172375081..172375105,+!p1@Tfap2c!2.05!111.48!Tfap2c;;chr8:26958093..26958148,-!p2@Ash2l!2.04!107.45!Ash2l;;chr2:103264213..103264233,+!p1@Elf5!1.93!84.78!Elf5;;chr19:5447886..5447905,+!p1@Fosl1!1.92!81.26!Fosl1;;chrX:35180221..35180224,+!p1@Rhox6!1.91!81.09!Rhox6;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.68!59.77!Zbtb11;;chrX:133654344..133654358,-!p2@Esx1!1.67!45.33!Esx1;;chr19:5447692..5447711,+!p2@Fosl1!1.64!42.98!Fosl1;;chr8:77540128..77540145,+!p2@Hmgxb4!1.61!39.45!Hmgxb4;;chr7:147129777..147129814,+!p2@Utf1!1.60!38.45!Utf1;;chr2:172375136..172375149,+!p2@Tfap2c!1.55!34.75!Tfap2c;;chr2:103264245..103264268,+!p2@Elf5!1.52!32.07!Elf5;;chrX:98449898..98449913,+!p2@Foxo4!1.51!98.38!Foxo4;;chr4:124334894..124334899,+!p1@Pou3f1!1.49!38.28!Pou3f1;;chr9:118387300..118387317,+!p1@Eomes!1.49!30.22!Eomes;;chr8:77540157..77540170,+!p3@Hmgxb4!1.46!27.87!Hmgxb4;;chr11:57645586..57645597,-!p2@Hand1!1.46!27.53!Hand1;;chr13:53568104..53568156,-!p1@Msx2!1.45!39.79!Msx2;;chr12:87811081..87811100,+!p2@Esrrb!1.45!26.86!Esrrb;;chr5:148118639..148118715,-!p1@Cdx2!1.44!26.69!Cdx2;;chr6:88148650..88148669,+!p1@Gata2!1.43!209.69!Gata2;;chrX:48499591..48499593,-!p3@Mbnl3!1.43!26.02!Mbnl3;;chr12:87811059..87811072,+!p3@Esrrb!1.42!25.52!Esrrb;;chr2:153475178..153475196,+!p1@Dnmt3b!1.40!50.03!Dnmt3b;;chr11:69468531..69468557,+!p1@Sox15!1.40!24.18!Sox15;;chrX:133654245..133654253,-!p3@Esx1!1.37!22.66!Esx1;;chr10:127095407..127095440,+!p3@Stat6!1.33!25.18!Stat6;;chr2:9800207..9800234,-!p1@Gata3!1.31!57.92!Gata3;;chr9:118387969..118387984,+!p2@Eomes!1.28!18.13!Eomes;;chr7:20162663..20162678,+!p1@Zfp296!1.26!22.83!Zfp296;;chr10:79390075..79390115,+!p2@Arid3a!1.23!53.05!Arid3a;;chr2:172376528..172376543,+!p3@Tfap2c!1.23!16.12!Tfap2c;;chr2:162880387..162880413,+!p1@Mybl2!1.20!91.33!Mybl2;;chr3:34548909..34548927,+!p1@Sox2!1.20!24.85!Sox2;;chr6:115311270..115311298,+!p1@Pparg!1.20!21.66!Pparg;;chr6:128250380..128250442,-!p2@Tead4!1.18!17.96!Tead4;;chr11:94981424..94981439,+!p1@Dlx3!1.17!15.61!Dlx3;;chrX:133654667..133654672,-!p1@Esx1!1.17!13.77!Esx1;;chr7:147129680..147129693,+!p3@Utf1!1.16!13.43!Utf1;;chrX:35464090..35464097,-!p1@Rhox12!1.16!13.43!Rhox12;;chr1:137155026..137155042,-!p1@Elf3!1.14!73.37!Elf3;;chr6:128250471..128250519,-!p1@Tead4!1.12!24.18!Tead4;;chr2:168592636..168592651,-!p1@Sall4!1.11!11.92!Sall4;;chr7:19946556..19946611,+!p1@Ppp1r13l!1.10!45.66!Ppp1r13l;;chr13:40829137..40829205,-!p1@Tfap2a!1.10!13.10!Tfap2a;;chr8:44392345..44392363,-!p1@Zfp42!1.09!11.42!Zfp42;;chr9:119893782..119893802,-!p1@Csrnp1!1.06!10.58!Csrnp1;;chr13:44825008..44825066,+!p5@Jarid2!1.02!18.80!Jarid2;;chr8:94325814..94325839,-!p2@Irx3!1.01!19.64!Irx3;;chr2:153475210..153475252,+!p2@Dnmt3b!1.00!25.52!Dnmt3b;;chr8:94325847..94325869,-!p3@Irx3!0.98!13.77!Irx3;;chr8:44392374..44392389,-!p2@Zfp42!0.96!8.06!Zfp42;;chr2:103264277..103264292,+!p3@Elf5!0.96!8.06!Elf5;;chr16:17233653..17233683,+!p1@Hic2!0.94!50.87!Hic2;;chr13:53568191..53568219,-!p2@Msx2!0.94!7.72!Msx2;;chr1:57029281..57029326,-!p1@Satb2!0.91!11.42!Satb2;;chr17:28409136..28409150,+!p3@Ppard!0.91!7.22!Ppard;;chr6:72739034..72739055,-!p3@Tcf7l1!0.90!15.61!Tcf7l1;;chr7:150155143..150155156,-!p1@Ascl2!0.90!6.88!Ascl2;;chr9:118387742..118387753,+!p3@Eomes!0.90!6.88!Eomes;;chr8:94325321..94325366,-!p1@Irx3!0.88!16.45!Irx3;;chr13:72766279..72766296,+!p2@Irx2!0.88!9.91!Irx2;;chr14:118636214..118636235,-!p1@Sox21!0.88!8.06!Sox21;;chr12:57714257..57714278,-!p1@Nkx2-9!0.86!6.21!Nkx2-9;;chr4:54957910..54957954,+!p2@Zfp462!0.84!18.80!Zfp462;;chr3:99057269..99057306,+!p1@Tbx15!0.84!7.39!Tbx15;;chr4:46356509..46356527,+!p1@Foxe1!0.84!5.88!Foxe1;;chr12:57714288..57714305,-!p2@Nkx2-9!0.84!5.88!Nkx2-9;;chr11:69468501..69468515,+!p2@Sox15!0.84!5.88!Sox15;;chr2:167363692..167363710,+!p1@Snai1!0.83!75.72!Snai1;;chr17:84105510..84105540,+!p2@Mta3!0.83!32.74!Mta3;;chr18:36441119..36441158,+!p2@Pura!0.83!14.61!Pura;;chr9:24578720..24578735,-!p1@Tbx20!0.83!5.71!Tbx20;;chr10:107769168..107769215,+!p1@Pawr!0.81!59.26!Pawr;;chrX:103123886..103123922,-!p3@Atrx!0.81!15.45!Atrx;;chr6:128250521..128250543,-!p3@Tead4!0.81!8.90!Tead4;;chr4:135129447..135129467,-!p2@Grhl3!0.80!6.55!Grhl3;;chrX:83437105..83437121,+!p1@Nr0b1!0.80!5.37!Nr0b1;;chr16:55822241..55822258,-!p1@Nfkbiz!0.78!171.07!Nfkbiz;;chr12:86814833..86814846,+!p1@Fos!0.78!128.26!Fos;;chr2:31428221..31428244,+!p2@Fubp3!0.78!13.10!Fubp3;;chr11:52096804..52096896,-!p1@Tcf7!0.77!43.15!Tcf7;;chr15:76500241..76500250,-!p@chr15:76500241..76500250,-!0.77!4.87!Foxh1;;chr14:118636238..118636257,-!p2@Sox21!0.77!4.87!Sox21;;chr2:168592591..168592604,-!p2@Sall4!0.76!4.70!Sall4;;chr2:9800094..9800108,-!p3@Gata3!0.76!4.70!Gata3;;chr16:50432467..50432522,-!p1@Bbx!0.75!99.39!Bbx;;chr2:32219200..32219213,+!p5@Ciz1!0.75!6.21!Ciz1;;chr2:162880327..162880385,+!p2@Mybl2!0.74!33.07!Mybl2;;chr7:119822957..119822980,+!p2@Tead1!0.74!24.01!Tead1;;chr13:72766250..72766273,+!p1@Irx2!0.74!7.39!Irx2;;chr11:96880072..96880079,+!p1@Sp6!0.74!4.53!Sp6;;chr2:162880418..162880429,+!p4@Mybl2!0.73!5.71!Mybl2;;chr16:55966451..55966484,+!p3@Rpl24,p3@Zbtb11!0.72!28.20!Zbtb11;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.72!13.43!Tfcp2l1;;chr13:72101178..72101203,-!p1@Irx1!0.71!6.72!Irx1;;chr15:76709662..76709676,+!p2@Zfp7!0.70!9.07!Zfp7;;chr8:124984566..124984595,-!p1@Snai3!0.70!6.55!Snai3;;chr10:79390120..79390129,+!p4@Arid3a!0.70!4.53!Arid3a;;chr8:26958153..26958170,-!p5@Ash2l!0.70!4.03!Ash2l;;chr1:135557400..135557421,-!p4@Zbed6!0.70!4.03!Zbed6;;chr5:77524231..77524245,-!p3@Hopx!0.69!10.74!Hopx;;chr7:19946535..19946550,+!p3@Ppp1r13l!0.69!6.21!Ppp1r13l;;chr8:94325486..94325510,-!p4@Irx3!0.69!5.37!Irx3;;chr15:37162834..37162849,+!p2@Grhl2!0.69!4.70!Grhl2;;chr14:122874619..122874634,+!p1@Zic2!0.69!3.86!Zic2;;chr13:53568081..53568094,-!p3@Msx2!0.69!3.86!Msx2;;chr6:140571128..140571148,+!p10@Aebp2!0.69!3.86!Aebp2;;chr3:32264565..32264613,-!p1@Zmat3!0.68!48.02!Zmat3;;chr19:41557591..41557634,+!p3@Lcor!0.68!10.74!Lcor;;chr4:135129538..135129558,-!p1@Grhl3!0.68!6.04!Grhl3;;chr6:72739185..72739232,-!p1@Tcf7l1!0.67!43.65!Tcf7l1;;chr19:46379199..46379301,+!p1@Nfkb2!0.67!24.18!Nfkb2;;chr5:77524199..77524210,-!p10@Hopx!0.67!3.69!Hopx;;chr7:19945089..19945107,+!p2@Ppp1r13l!0.66!6.21!Ppp1r13l;;chr14:99697871..99697934,+!p1@Klf5!0.65!79.75!Klf5;;chr2:83484634..83484647,+!p4@Zc3h15!0.65!27.87!Zc3h15;;chr11:101645830..101645881,-!p2@Etv4!0.65!6.88!Etv4;;chr17:48025139..48025166,-!p8@Foxp4!0.64!4.03!Foxp4;;chr17:47922678..47922688,+!p10@Tfeb!0.64!3.36!Tfeb;;chr19:5447859..5447866,+!p3@Fosl1!0.64!3.36!Fosl1;;chr1:57029076..57029098,-!p8@Satb2!0.64!3.36!Satb2;;chr1:135557383..135557395,-!p5@Zbed6!0.64!3.36!Zbed6;;chr17:84105477..84105509,+!p3@Mta3!0.62!14.44!Mta3;;chr16:55966407..55966447,+!p6@Rpl24,p6@Zbtb11!0.62!8.56!Zbtb11;;chrX:48559194..48559210,-!p4@Mbnl3!0.62!4.20!Mbnl3;;chr18:75527009..75527027,+!p1@Smad7!0.61!77.56!Smad7;;chr7:6238191..6238224,+!p1@Zfp667!0.61!21.83!Zfp667;;chr3:90097275..90097302,+!p2@Gatad2b!0.61!8.06!Gatad2b;;chr3:32264530..32264544,-!p2@Zmat3!0.61!5.20!Zmat3;;chr4:107107175..107107204,+!p1@Glis1!0.61!3.86!Glis1;;chr5:77695241..77695257,+!p10@Rest!0.61!3.53!Rest;;chr13:37917716..37917742,+!p9@Rreb1!0.60!5.71!Rreb1;;chr10:80809447..80809515,-!p5@Hmg20b!0.60!3.86!Hmg20b;;chr11:57645644..57645649,-!p3@Hand1!0.60!3.02!Hand1;;chr8:44392404..44392412,-!p3@Zfp42!0.60!3.02!Zfp42;;chr12:75009172..75009223,+!p3@Hif1a!0.59!8.23!Hif1a;;chr10:107769750..107769799,+!p2@Pawr!0.59!7.05!Pawr;;chr15:37162796..37162828,+!p1@Grhl2!0.59!5.37!Grhl2;;chr3:128917187..128917223,+!p2@Pitx2!0.59!3.53!Pitx2;;chr6:52108291..52108323,-!p1@Hoxa1!0.59!2.85!Hoxa1;;chr9:106356211..106356242,+!p1@Pcbp4!0.58!67.32!Pcbp4;;chrX:103124643..103124660,-!p2@Atrx!0.58!23.17!Atrx;;chr3:32409460..32409483,+!p2@Zfp639!0.58!15.61!Zfp639;;chr11:101646566..101646603,-!p1@Etv4!0.58!10.58!Etv4;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.58!4.20!Carhsp1;;chr8:94325273..94325288,-!p5@Irx3!0.58!3.69!Irx3;;chr17:28409059..28409076,+!p6@Ppard!0.57!2.69!Ppard;;chrX:58146612..58146615,-!p1@Sox3!0.57!2.69!Sox3;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.56!155.13!Hmga1;;chr17:51971932..51971958,-!p2@Satb1!0.56!3.86!Satb1;;chr3:99057256..99057268,+!p3@Tbx15!0.55!2.52!Tbx15;;chr13:48758276..48758291,+!p1@Barx1!0.55!2.52!Barx1;;chr8:44392310..44392319,-!p4@Zfp42!0.55!2.52!Zfp42;;chr13:30076280..30076334,-!p3@E2f3!0.54!8.73!E2f3;;chr5:21290933..21291050,-!p1@Dnajc2!0.53!114.83!Dnajc2;;chr7:19895384..19895399,-!p2@Fosb!0.53!3.69!Fosb;;chr9:118387933..118387942,+!p4@Eomes!0.53!2.35!Eomes;;chr13:40826961..40827001,-!p4@Tfap2a!0.53!2.35!Tfap2a;;chr11:96829969..96829987,-!p2@Sp2!0.53!2.35!Sp2;;chr17:51971991..51972003,-!p4@Satb1!0.53!2.35!Satb1;;chr5:77524175..77524186,-!p8@Hopx!0.53!2.35!Hopx;;chr7:147129659..147129668,+!p4@Utf1!0.53!2.35!Utf1;;chrX:55283799..55283813,+!p1@Zic3!0.53!2.35!Zic3;;chr7:30906934..30907020,+!p1@Zfp382!0.52!19.64!Zfp382;;chr4:54957886..54957907,+!p3@Zfp462!0.52!4.53!Zfp462;;chr12:85534778..85534812,-!p3@C130039O16Rik!0.51!8.06!C130039O16Rik;;chr6:145814003..145814056,-!p1@Bhlhe41!0.51!7.89!Bhlhe41;;chr8:72520225..72520248,-!p9@Gatad2a!0.51!7.39!Gatad2a;;chr17:13897299..13897342,+!p3@Mllt4!0.51!6.21!Mllt4;;chr16:50429979..50429997,-!p4@Bbx!0.51!4.03!Bbx;;chr2:180377386..180377462,-!p1@Tcfl5!0.51!2.85!Tcfl5;;chr2:156665817..156665877,+!p1@Tgif2!0.50!17.96!Tgif2;;chr17:28369739..28369774,+!p2@Ppard!0.50!8.39!Ppard;;chr11:53164533..53164548,+!p4@Aff4!0.50!7.72!Aff4;;chr6:38204214..38204267,-!p4@D630045J12Rik!0.50!4.70!D630045J12Rik;;chr10:107769229..107769238,+!p3@Pawr!0.50!3.36!Pawr;;chr2:172376261..172376267,+!p4@Tfap2c!0.50!2.18!Tfap2c;;chr2:168780729..168780740,-!p3@LOC100502777,p3@Zfp64!0.50!2.18!Zfp64;;chr13:53568169..53568179,-!p4@Msx2!0.50!2.18!Msx2;;chr14:122874593..122874610,+!p2@Zic2!0.50!2.18!Zic2;;chr14:118635860..118635885,-!p3@Sox21!0.50!2.18!Sox21;;chr17:28487692..28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 |fonse_cell_line=FF:0000626
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011201
 |is_obsolete=
-|name=trophoblast stem cell line Rybp differentiation, day00, biol_rep1
+|library_id=CNhs13519
+|library_id_phase_based=2:CNhs13519
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;13290
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;13290
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520Rybp%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13519.13290-142G5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520Rybp%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13519.13290-142G5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520Rybp%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13519.13290-142G5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520Rybp%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13519.13290-142G5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520Rybp%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13519.13290-142G5.mm9.nobarcode.rdna.fa.gz
+|name=trophoblast stem cell line Rybp differentiation
 |namespace=
 |part_of=
 |profile_cagescan=,,,
 |profile_hcage=CNhs13519,LSID1025,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.196433817784095,0,0,0,0,1.20120508872074,0,0,0,0,0,0,0.0312230241490387,0,0,0,0,0,0,0,0,0,0,0,0,0.0673999378519914,-0.220925132203512,0,0,0,0,0,-0.112757038581409,-0.0710880390786407,0.179362721353824,-0.916811428625835,-0.269868638010351,0.337497660120519,0,0,0,0,0,0,0,0,0,0,0,0.0597258884134036,2.53696734590132,0,0,0,-0.0428469550828748,0,-0.0191383779349801,0,0,-0.022966549103376,-0.0499898650563348,-0.133502786995636,-0.158091042771083,-0.0365927089968535,0,-0.01060866289996,-0.102616055146161,0,0,0,-0.08383775793894,-0.188873989919988,0.0755783845540881,-0.0114316569879161,0,0,0,0,0,0,-0.00564701182441457,-0.045664345787777,0.409146693112219,0,0,0,0.125731435976844,0
 |rna_box=142
 |rna_catalog_number=
@@ Line 56: / Line 74: @@
 |rna_sample_type=
 |rna_tube_id=142G5
-|rna_weight_ug=51.00
+|rna_weight_ug=51
 |sample_age=
+|sample_category=time courses
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 95: @@
 |sample_strain=
 |sample_tissue=
+|time= day00
+|timecourse=trophoblast_differentiation
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:13290-142G5;search_select_hide=table117:13290-142G5
 }}

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FF:13290-142G5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:55, 4 June 2020

CNhs13519

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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