FF:13297-142H3: Difference between revisions

Latest revision as of 18:55, 4 June 2020

Name:	trophoblast stem cell line B1 differentiation
Species:	Mouse (Mus musculus)
Library ID:	CNhs13526
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	female
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	B1 +d0
catalog number	NA
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005070

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13526		CAGE		DRX008916		DRR009790

Accession ID Mm9

Library id		BAM		CTSS
CNhs13526		DRZ001215		DRZ002598

Accession ID Mm10

Library id		BAM		CTSS
CNhs13526		DRZ012565		DRZ013948

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

CNhs13526

0	0
1	0
10	0
100	0
1000	0
1001	-0.0356
1002	-0.102
1003	-0.175
1004	0
1005	-0.294
1006	-0.147
1007	-0.115
1008	0
1009	-0.161
101	0.333
1010	0
1011	-0.178
1012	0
1013	-0.153
1014	-0.0874
1015	-0.132
1016	-0.292
1017	0
1018	0.736
1019	0
102	0
1020	0.222
1021	0.111
1022	-0.0704
1023	0
1024	-0.14
1025	0
1026	0
1027	-0.048
1028	0
1029	-0.115
103	-0.0861
1030	0
1031	-0.508
1032	-0.293
1033	0
1034	0
1035	0
1036	0.105
1037	0
1038	-0.112
1039	-0.189
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: CNhs13526

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.253
MA0003.1	MA0003.1	0.663
MA0004.1	MA0004.1	0.126
MA0006.1	MA0006.1	0.987
MA0007.1	MA0007.1	0.861
MA0009.1	MA0009.1	0.34
MA0014.1	MA0014.1	0.0931
MA0017.1	MA0017.1	0.981
MA0018.2	MA0018.2	0.00345
MA0019.1	MA0019.1	0.679
MA0024.1	MA0024.1	1.00463e-4
MA0025.1	MA0025.1	0.7
MA0027.1	MA0027.1	0.789
MA0028.1	MA0028.1	7.57934e-7
MA0029.1	MA0029.1	0.00397
MA0030.1	MA0030.1	0.659
MA0031.1	MA0031.1	0.3
MA0035.2	MA0035.2	0.391
MA0038.1	MA0038.1	0.635
MA0039.2	MA0039.2	8.12767e-6
MA0040.1	MA0040.1	0.755
MA0041.1	MA0041.1	0.163
MA0042.1	MA0042.1	0.43
MA0043.1	MA0043.1	0.00229
MA0046.1	MA0046.1	3.94587e-11
MA0047.2	MA0047.2	0.0219
MA0048.1	MA0048.1	0.0303
MA0050.1	MA0050.1	0.0386
MA0051.1	MA0051.1	0.809
MA0052.1	MA0052.1	1.28317e-4
MA0055.1	MA0055.1	1.04279e-5
MA0057.1	MA0057.1	0.978
MA0058.1	MA0058.1	0.0616
MA0059.1	MA0059.1	0.0185
MA0060.1	MA0060.1	3.00502e-5
MA0061.1	MA0061.1	0.54
MA0062.2	MA0062.2	2.96043e-9
MA0065.2	MA0065.2	0.288
MA0066.1	MA0066.1	0.942
MA0067.1	MA0067.1	0.306
MA0068.1	MA0068.1	0.00324
MA0069.1	MA0069.1	0.551
MA0070.1	MA0070.1	0.402
MA0071.1	MA0071.1	0.053
MA0072.1	MA0072.1	0.495
MA0073.1	MA0073.1	0.609
MA0074.1	MA0074.1	0.775
MA0076.1	MA0076.1	4.17421e-6
MA0077.1	MA0077.1	0.369
MA0078.1	MA0078.1	0.176
MA0079.2	MA0079.2	0.193
MA0080.2	MA0080.2	0.198
MA0081.1	MA0081.1	0.796
MA0083.1	MA0083.1	2.47107e-5
MA0084.1	MA0084.1	0.616
MA0087.1	MA0087.1	0.606
MA0088.1	MA0088.1	0.161
MA0090.1	MA0090.1	0.3
MA0091.1	MA0091.1	0.953
MA0092.1	MA0092.1	0.33
MA0093.1	MA0093.1	0.118
MA0099.2	MA0099.2	5.37098e-8
MA0100.1	MA0100.1	0.0253
MA0101.1	MA0101.1	0.154
MA0102.2	MA0102.2	0.835
MA0103.1	MA0103.1	0.0555
MA0104.2	MA0104.2	0.0212
MA0105.1	MA0105.1	0.172
MA0106.1	MA0106.1	0.0133
MA0107.1	MA0107.1	0.688
MA0108.2	MA0108.2	0.0461
MA0111.1	MA0111.1	0.473
MA0112.2	MA0112.2	0.735
MA0113.1	MA0113.1	0.566
MA0114.1	MA0114.1	0.932
MA0115.1	MA0115.1	0.00853
MA0116.1	MA0116.1	0.269
MA0117.1	MA0117.1	0.695
MA0119.1	MA0119.1	7.02101e-4
MA0122.1	MA0122.1	0.623
MA0124.1	MA0124.1	0.437
MA0125.1	MA0125.1	0.158
MA0131.1	MA0131.1	0.0847
MA0135.1	MA0135.1	0.258
MA0136.1	MA0136.1	0.0392
MA0137.2	MA0137.2	0.0107
MA0138.2	MA0138.2	0.0234
MA0139.1	MA0139.1	0.185
MA0140.1	MA0140.1	0.0402
MA0141.1	MA0141.1	0.655
MA0142.1	MA0142.1	0.993
MA0143.1	MA0143.1	0.533
MA0144.1	MA0144.1	0.314
MA0145.1	MA0145.1	0.696
MA0146.1	MA0146.1	0.0237
MA0147.1	MA0147.1	0.0118
MA0148.1	MA0148.1	0.0125
MA0149.1	MA0149.1	0.0295
MA0150.1	MA0150.1	0.222
MA0152.1	MA0152.1	0.0123
MA0153.1	MA0153.1	9.32528e-6
MA0154.1	MA0154.1	0.152
MA0155.1	MA0155.1	0.357
MA0156.1	MA0156.1	0.0163
MA0157.1	MA0157.1	0.175
MA0159.1	MA0159.1	0.289
MA0160.1	MA0160.1	0.101
MA0162.1	MA0162.1	0.887
MA0163.1	MA0163.1	0.759
MA0164.1	MA0164.1	0.0574
MA0258.1	MA0258.1	0.966
MA0259.1	MA0259.1	0.0324

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: CNhs13526

Novel motif	Logo	P-value
1	1	0.563
10	10	0.644
100	100	0.353
101	101	0.0931
102	102	0.156
103	103	0.736
104	104	0.787
105	105	0.36
106	106	0.232
107	107	0.0917
108	108	0.666
109	109	0.576
11	11	0.849
110	110	0.9
111	111	0.14
112	112	0.647
113	113	0.614
114	114	0.409
115	115	0.434
116	116	0.811
117	117	4.39016e-4
118	118	0.332
119	119	0.577
12	12	0.446
120	120	0.792
121	121	0.414
122	122	0.489
123	123	0.00278
124	124	0.0931
125	125	0.847
126	126	0.287
127	127	0.48
128	128	0.176
129	129	0.823
13	13	0.0296
130	130	0.248
131	131	0.0158
132	132	0.171
133	133	0.174
134	134	0.185
135	135	0.0209
136	136	0.016
137	137	0.523
138	138	0.685
139	139	0.278
14	14	0.465
140	140	0.102
141	141	0.907
142	142	0.606
143	143	0.562
144	144	0.573
145	145	0.36
146	146	0.605
147	147	0.97
148	148	0.0134
149	149	0.00984
15	15	0.466
150	150	0.649
151	151	0.0864
152	152	0.0823
153	153	0.663
154	154	0.943
155	155	0.0256
156	156	0.0555
157	157	0.765
158	158	0.281
159	159	0.948
160	160	0.552
161	161	0.246
162	162	0.209
163	163	0.183
164	164	0.0247
165	165	0.424
166	166	0.00385
167	167	0.662
168	168	0.271
169	169	0.868
17	17	0.877
18	18	0.384
19	19	0.282
2	2	0.0787
20	20	0.00709
21	21	0.472
22	22	0.952
23	23	0.109
24	24	0.338
25	25	0.922
26	26	0.326
27	27	0.0554
28	28	0.775
29	29	0.00391
3	3	0.948
30	30	0.538
31	31	0.362
32	32	0.024
33	33	0.465
34	34	0.614
35	35	0.379
36	36	0.582
37	37	0.64
38	38	0.776
39	39	0.484
4	4	0.0636
40	40	0.391
41	41	0.18
42	42	0.852
43	43	0.371
44	44	0.181
45	45	0.541
46	46	0.849
47	47	0.765
48	48	0.724
49	49	0.43
5	5	0.345
50	50	0.903
51	51	0.568
52	52	0.274
53	53	0.0409
54	54	0.692
55	55	0.186
56	56	0.491
57	57	0.891
58	58	0.784
59	59	0.334
6	6	0.662
60	60	0.528
61	61	0.11
62	62	0.916
63	63	0.245
64	64	0.521
65	65	0.458
66	66	0.504
67	67	0.328
68	68	0.222
69	69	0.137
7	7	0.983
70	70	0.86
71	71	0.942
72	72	0.762
73	73	0.0437
74	74	0.248
75	75	0.167
76	76	0.0215
77	77	0.653
78	78	0.524
79	79	0.87
8	8	0.706
80	80	0.229
81	81	0.132
82	82	0.313
83	83	0.701
84	84	0.328
85	85	0.314
86	86	0.85
87	87	0.0604
88	88	0.0465
89	89	0.81
9	9	0.378
90	90	0.996
91	91	0.166
92	92	0.356
93	93	0.133
94	94	0.548
95	95	0.0839
96	96	0.914
97	97	0.902
98	98	0.0721
99	99	0.0809

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: CNhs13526

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011275 mouse trophoblast stem cell line B1 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)
0000383 (3 days sample)
0000626 (trophoblast cell line sample)
0000643 (mouse trophoblast stem cell line R1AB sample)
0011275 (mouse trophoblast stem cell line B1 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@SAMD00005070
+|accession_numbers=CAGE;DRX008916;DRR009790;DRZ001215;DRZ002598;DRZ012565;DRZ013948
 |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:0000383,FF:0000626,FF:0000643,FF:0011275
 |comment=
 |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!2.55!356.73!Hand1;;chr7:147129712..147129774,+!p1@Utf1!2.43!269.27!Utf1;;chr2:103264213..103264233,+!p1@Elf5!2.11!127.42!Elf5;;chr8:26958093..26958148,-!p2@Ash2l!2.01!101.23!Ash2l;;chr12:87811081..87811100,+!p2@Esrrb!1.87!73.70!Esrrb;;chr2:172375081..172375105,+!p1@Tfap2c!1.84!68.37!Tfap2c;;chr2:153475178..153475196,+!p1@Dnmt3b!1.78!121.87!Dnmt3b;;chr12:87811059..87811072,+!p3@Esrrb!1.76!56.83!Esrrb;;chr7:147129777..147129814,+!p2@Utf1!1.73!52.83!Utf1;;chr2:103264245..103264268,+!p2@Elf5!1.73!52.39!Elf5;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.65!54.83!Zbtb11;;chr8:77540128..77540145,+!p2@Hmgxb4!1.65!43.95!Hmgxb4;;chr4:124334894..124334899,+!p1@Pou3f1!1.64!55.05!Pou3f1;;chr9:118387300..118387317,+!p1@Eomes!1.61!40.18!Eomes;;chrX:35180221..35180224,+!p1@Rhox6!1.61!39.29!Rhox6;;chr8:77540157..77540170,+!p3@Hmgxb4!1.60!38.63!Hmgxb4;;chrX:133654344..133654358,-!p2@Esx1!1.60!38.40!Esx1;;chr13:53568104..53568156,-!p1@Msx2!1.55!50.83!Msx2;;chrX:83437105..83437121,+!p1@Nr0b1!1.50!30.63!Nr0b1;;chr19:5447886..5447905,+!p1@Fosl1!1.49!30.19!Fosl1;;chr9:118387969..118387984,+!p2@Eomes!1.49!29.75!Eomes;;chr5:148118639..148118715,-!p1@Cdx2!1.48!29.52!Cdx2;;chrX:98449898..98449913,+!p2@Foxo4!1.41!77.25!Foxo4;;chr3:34548909..34548927,+!p1@Sox2!1.40!40.62!Sox2;;chr6:88148650..88148669,+!p1@Gata2!1.37!180.47!Gata2;;chr2:9800207..9800234,-!p1@Gata3!1.36!64.60!Gata3;;chr2:103264277..103264292,+!p3@Elf5!1.36!21.75!Elf5;;chr2:153475210..153475252,+!p2@Dnmt3b!1.34!55.94!Dnmt3b;;chr10:127095407..127095440,+!p3@Stat6!1.34!25.75!Stat6;;chr2:162880387..162880413,+!p1@Mybl2!1.26!107.00!Mybl2;;chr11:57645586..57645597,-!p2@Hand1!1.25!16.65!Hand1;;chr6:128250471..128250519,-!p1@Tead4!1.22!31.30!Tead4;;chr7:147129680..147129693,+!p3@Utf1!1.22!15.76!Utf1;;chr6:128250380..128250442,-!p2@Tead4!1.20!18.65!Tead4;;chr9:119893782..119893802,-!p1@Csrnp1!1.18!13.99!Csrnp1;;chr2:172375136..172375149,+!p2@Tfap2c!1.16!13.54!Tfap2c;;chr7:20162663..20162678,+!p1@Zfp296!1.14!16.87!Zfp296;;chr19:5447692..5447711,+!p2@Fosl1!1.14!12.88!Fosl1;;chr2:168592636..168592651,-!p1@Sall4!1.14!12.65!Sall4;;chr11:94981424..94981439,+!p1@Dlx3!1.12!13.76!Dlx3;;chr8:44392345..44392363,-!p1@Zfp42!1.10!11.54!Zfp42;;chr14:118636214..118636235,-!p1@Sox21!1.09!13.54!Sox21;;chr14:118636238..118636257,-!p2@Sox21!1.09!11.32!Sox21;;chr8:44392374..44392389,-!p2@Zfp42!1.09!11.32!Zfp42;;chr11:69468531..69468557,+!p1@Sox15!1.07!10.66!Sox15;;chr9:24578720..24578735,-!p1@Tbx20!1.06!10.43!Tbx20;;chrX:133654245..133654253,-!p3@Esx1!1.06!10.43!Esx1;;chr10:79390075..79390115,+!p2@Arid3a!1.04!33.74!Arid3a;;chr9:118387742..118387753,+!p3@Eomes!1.04!9.99!Eomes;;chr1:137155026..137155042,-!p1@Elf3!1.03!56.83!Elf3;;chr2:172376528..172376543,+!p3@Tfap2c!1.03!9.77!Tfap2c;;chr12:87762578..87762612,+!p1@Esrrb!1.02!9.55!Esrrb;;chr7:19946556..19946611,+!p1@Ppp1r13l!1.01!37.07!Ppp1r13l;;chr13:40829137..40829205,-!p1@Tfap2a!0.99!9.99!Tfap2a;;chr13:44825008..44825066,+!p5@Jarid2!0.97!16.65!Jarid2;;chr14:122874619..122874634,+!p1@Zic2!0.97!8.44!Zic2;;chr2:162880327..162880385,+!p2@Mybl2!0.96!55.27!Mybl2;;chr4:135129447..135129467,-!p2@Grhl3!0.96!9.99!Grhl3;;chr14:99697871..99697934,+!p1@Klf5!0.95!161.61!Klf5;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.94!22.86!Tfcp2l1;;chr8:124984566..124984595,-!p1@Snai3!0.94!12.21!Snai3;;chrX:48499591..48499593,-!p3@Mbnl3!0.94!7.77!Mbnl3;;chr4:54957910..54957954,+!p2@Zfp462!0.93!23.53!Zfp462;;chr6:128250521..128250543,-!p3@Tead4!0.93!11.99!Tead4;;chrX:133654667..133654672,-!p1@Esx1!0.93!7.55!Esx1;;chrX:103123886..103123922,-!p3@Atrx!0.91!19.76!Atrx;;chr4:135129538..135129558,-!p1@Grhl3!0.91!11.10!Grhl3;;chr16:17233653..17233683,+!p1@Hic2!0.90!46.40!Hic2;;chr2:31428221..31428244,+!p2@Fubp3!0.90!17.54!Fubp3;;chr1:57029281..57029326,-!p1@Satb2!0.89!10.66!Satb2;;chr13:53568191..53568219,-!p2@Msx2!0.88!6.66!Msx2;;chr6:72739034..72739055,-!p3@Tcf7l1!0.86!13.99!Tcf7l1;;chr11:101645830..101645881,-!p2@Etv4!0.86!11.77!Etv4;;chr3:99057269..99057306,+!p1@Tbx15!0.85!7.55!Tbx15;;chr2:162880306..162880319,+!p3@Mybl2!0.83!8.44!Mybl2;;chr12:57714288..57714305,-!p2@Nkx2-9!0.83!5.77!Nkx2-9;;chr4:149611832..149611846,+!p3@LOC100045967,p3@LOC100503183,p4@Eno1,p4@Gm5506!0.82!5.55!Eno1;;chr13:72766250..72766273,+!p1@Irx2!0.81!8.66!Irx2;;chr10:107769168..107769215,+!p1@Pawr!0.79!57.49!Pawr;;chr17:84105510..84105540,+!p2@Mta3!0.79!29.97!Mta3;;chr8:26958153..26958170,-!p5@Ash2l!0.79!5.11!Ash2l;;chr3:32264565..32264613,-!p1@Zmat3!0.78!60.60!Zmat3;;chr7:19946535..19946550,+!p3@Ppp1r13l!0.78!7.99!Ppp1r13l;;chr8:13338745..13338756,+!p2@Tfdp1!0.76!11.54!Tfdp1;;chr11:52096804..52096896,-!p1@Tcf7!0.75!41.29!Tcf7;;chr11:101646566..101646603,-!p1@Etv4!0.75!16.43!Etv4;;chr7:147129659..147129668,+!p4@Utf1!0.75!4.66!Utf1;;chr2:9800094..9800108,-!p3@Gata3!0.75!4.66!Gata3;;chr18:75527009..75527027,+!p1@Smad7!0.74!104.33!Smad7;;chr17:37139472..37139514,+!p1@Zfp57!0.74!33.52!Zfp57;;chr8:94325814..94325839,-!p2@Irx3!0.74!9.99!Irx3;;chr1:135557383..135557395,-!p5@Zbed6!0.74!4.44!Zbed6;;chr12:57714257..57714278,-!p1@Nkx2-9!0.74!4.44!Nkx2-9;;chr2:162880418..162880429,+!p4@Mybl2!0.72!5.55!Mybl2;;chr11:57645644..57645649,-!p3@Hand1!0.72!4.22!Hand1;;chr6:52108291..52108323,-!p1@Hoxa1!0.72!4.22!Hoxa1;;chr8:94325321..94325366,-!p1@Irx3!0.71!10.88!Irx3;;chrX:48559194..48559210,-!p4@Mbnl3!0.71!5.33!Mbnl3;;chr13:72766279..72766296,+!p2@Irx2!0.70!6.22!Irx2;;chr13:48758358..48758415,+!p2@Barx1!0.70!4.00!Barx1;;chr1:135557400..135557421,-!p4@Zbed6!0.70!4.00!Zbed6;;chrX:58146612..58146615,-!p1@Sox3!0.70!4.00!Sox3;;chr12:12948633..12948651,-!p1@Mycn!0.69!42.40!Mycn;;chr8:94325847..94325869,-!p3@Irx3!0.69!6.66!Irx3;;chr10:107769229..107769238,+!p3@Pawr!0.69!5.77!Pawr;;chr3:34548946..34548972,+!p2@Sox2!0.69!4.44!Sox2;;chr14:122874593..122874610,+!p2@Zic2!0.68!3.77!Zic2;;chr18:36441119..36441158,+!p2@Pura!0.67!9.99!Pura;;chr6:72739185..72739232,-!p1@Tcf7l1!0.66!43.07!Tcf7l1;;chr16:55966451..55966484,+!p3@Rpl24,p3@Zbtb11!0.66!24.42!Zbtb11;;chr15:76709662..76709676,+!p2@Zfp7!0.66!8.21!Zfp7;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.66!5.33!Carhsp1;;chr15:37162834..37162849,+!p2@Grhl2!0.66!4.44!Grhl2;;chr17:28409136..28409150,+!p3@Ppard!0.66!3.55!Ppard;;chr9:91260616..91260653,-!p2@Zic1!0.66!3.55!Zic1;;chr12:25780945..25780961,-!p1@Id2!0.65!691.26!Id2;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.65!190.46!Hmga1;;chr4:54957886..54957907,+!p3@Zfp462!0.65!6.44!Zfp462;;chr3:99057256..99057268,+!p3@Tbx15!0.64!3.33!Tbx15;;chr9:118387933..118387942,+!p4@Eomes!0.64!3.33!Eomes;;chr11:21901608..21901634,-!p1@Otx1!0.64!3.33!Otx1;;chr7:119822957..119822980,+!p2@Tead1!0.63!18.65!Tead1;;chr10:107769750..107769799,+!p2@Pawr!0.63!7.77!Pawr;;chr17:48025139..48025166,-!p8@Foxp4!0.63!4.00!Foxp4;;chr17:51971991..51972003,-!p4@Satb1!0.61!3.11!Satb1;;chrX:35464090..35464097,-!p1@Rhox12!0.61!3.11!Rhox12;;chr11:99092233..99092273,-!p2@Smarce1!0.60!17.09!Smarce1;;chr17:84105477..84105509,+!p3@Mta3!0.59!13.54!Mta3;;chr13:30076280..30076334,-!p3@E2f3!0.59!9.99!E2f3;;chr15:37162796..37162828,+!p1@Grhl2!0.59!5.33!Grhl2;;chr13:53568081..53568094,-!p3@Msx2!0.59!2.89!Msx2;;chr13:48758276..48758291,+!p1@Barx1!0.59!2.89!Barx1;;chr11:120624106..120624107,+!p13@Hmga1-rs1,p14@Hmga1!0.59!2.89!Hmga1;;chr11:69468501..69468515,+!p2@Sox15!0.59!2.89!Sox15;;chr7:108966820..108966835,+!p1@Phox2a!0.59!2.89!Phox2a;;chr5:148118614..148118625,-!p4@Cdx2!0.59!2.89!Cdx2;;chr12:86814833..86814846,+!p1@Fos!0.58!79.69!Fos;;chr13:37917716..37917742,+!p9@Rreb1!0.58!5.33!Rreb1;;chr11:120624132..120624143,+!p10@Hmga1,p9@Hmga1-rs1!0.58!3.77!Hmga1;;chr10:80809447..80809515,-!p5@Hmg20b!0.58!3.55!Hmg20b;;chr16:50432467..50432522,-!p1@Bbx!0.57!65.93!Bbx;;chrX:103124643..103124660,-!p2@Atrx!0.57!22.42!Atrx;;chr17:71202822..71202877,-!p3@Tgif1!0.57!9.32!Tgif1;;chr5:38611720..38611799,+!p1@Lyar!0.56!89.46!Lyar;;chr2:167363692..167363710,+!p1@Snai1!0.56!39.96!Snai1;;chr1:57028125..57028149,-!p2@Satb2!0.56!2.66!Satb2;;chr2:103264977..103264986,+!p6@Elf5!0.56!2.66!Elf5;;chr17:47922678..47922688,+!p10@Tfeb!0.56!2.66!Tfeb;;chr13:72766234..72766243,+!p3@Irx2!0.56!2.66!Irx2;;chr13:40826961..40827001,-!p4@Tfap2a!0.56!2.66!Tfap2a;;chr11:101645774..101645795,-!p9@Etv4!0.56!2.66!Etv4;;chr9:96653072..96653154,-!p1@Zbtb38!0.55!7.99!Zbtb38;;chr17:13897299..13897342,+!p3@Mllt4!0.55!6.88!Mllt4;;chr17:37139519..37139531,+!p5@Zfp57!0.55!3.11!Zfp57;;chr3:32409460..32409483,+!p2@Zfp639!0.54!14.21!Zfp639;;chr1:138521574..138521597,+!p3@Zfp281!0.54!6.88!Zfp281;;chr11:99092312..99092333,-!p4@Smarce1!0.54!4.00!Smarce1;;chrX:55283799..55283813,+!p1@Zic3!0.54!2.44!Zic3;;chr8:44392310..44392319,-!p4@Zfp42!0.54!2.44!Zfp42;;chr2:168592591..168592604,-!p2@Sall4!0.54!2.44!Sall4;;chr2:168780729..168780740,-!p3@LOC100502777,p3@Zfp64!0.54!2.44!Zfp64;;chr13:53568169..53568179,-!p4@Msx2!0.54!2.44!Msx2;;chr2:168780757..168780805,-!p1@LOC100502777,p1@Zfp64!0.53!44.40!Zfp64;;chr11:101413151..101413207,-!p1@Brca1!0.53!29.08!Brca1;;chr10:119913310..119913366,-!p1@Hmga2!0.53!23.75!Hmga2;;chr2:83484634..83484647,+!p4@Zc3h15!0.53!21.09!Zc3h15;;chr10:127984472..127984504,-!p2@Zc3h10!0.53!9.32!Zc3h10;;chr14:99698164..99698208,+!p2@Klf5!0.53!2.89!Klf5;;chr8:72498266..72498306,-!p3@Gatad2a!0.52!19.76!Gatad2a;;chr2:156666727..156666753,+!p2@Tgif2!0.52!3.77!Tgif2;;chr8:94325486..94325510,-!p4@Irx3!0.52!3.33!Irx3;;chr11:53583544..53583559,+!p1@Irf1!0.51!48.84!Irf1;;chr10:110182489..110182589,+!p1@E2f7!0.51!35.07!E2f7;;chr18:75527030..75527055,+!p2@Smad7!0.51!18.20!Smad7;;chr17:51971932..51971958,-!p2@Satb1!0.51!3.33!Satb1;;chr15:76500241..76500250,-!p@chr15:76500241..76500250,-!0.51!2.22!Foxh1;;chr11:96880072..96880079,+!p1@Sp6!0.51!2.22!Sp6;;chr1:57028157..57028173,-!p3@Satb2!0.51!2.22!Satb2;;chr5:77524199..77524210,-!p10@Hopx!0.51!2.22!Hopx;;chr5:21290933..21291050,-!p1@Dnajc2!0.50!108.77!Dnajc2;;chr4:133801494..133801519,-!p2@Zfp593!0.50!19.98!Zfp593;;chr2:156665817..156665877,+!p1@Tgif2!0.50!17.98!Tgif2;;chr12:85534778..85534812,-!p3@C130039O16Rik!0.50!7.99!C13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 |fonse_cell_line=FF:0000626
@@ Line 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011275
 |is_obsolete=
-|name=trophoblast stem cell line B1 differentiation, day00, biol_rep1
+|library_id=CNhs13526
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+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;13297
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;13297
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520B1%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13526.13297-142H3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520B1%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13526.13297-142H3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520B1%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13526.13297-142H3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520B1%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13526.13297-142H3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520B1%2520differentiation%252c%2520day00%252c%2520biol_rep1.CNhs13526.13297-142H3.mm9.nobarcode.rdna.fa.gz
+|name=trophoblast stem cell line B1 differentiation
 |namespace=
 |part_of=
 |profile_cagescan=,,,
 |profile_hcage=CNhs13526,LSID1025,release012,COMPLETED
-|profile_rnaseq=,,,
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 |rna_box=142
 |rna_catalog_number=
@@ Line 59: / Line 76: @@
 |rna_weight_ug=52.75
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+|sample_category=time courses
 |sample_cell_catalog=
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@@ Line 77: / Line 95: @@
 |sample_strain=
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+|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=table111:13297-142H3;search_select_hide=table117:13297-142H3
 }}

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FF:13297-142H3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:55, 4 June 2020

CNhs13526

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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