FF:12987-138I8: Difference between revisions

Latest revision as of 18:48, 4 June 2020

Name:	TSt-4/DLL1 feeder cells, biol_rep2
Species:	Mouse (Mus musculus)
Library ID:	CNhs13408
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	NA
age	NA
cell type	unclassifiable
cell line	NA
company	NA
collaboration	Tomokatsu Ikawa (RCAI)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005409

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13408		CAGE		DRX008909		DRR009783

Accession ID Mm9

Library id		BAM		CTSS
CNhs13408		DRZ001208		DRZ002591

Accession ID Mm10

Library id		BAM		CTSS
CNhs13408		DRZ012558		DRZ013941

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

CNhs13408

0	0
1	0
10	0
100	0
1000	0
1001	-0.0749
1002	0
1003	-0.175
1004	0
1005	-0.154
1006	-0.183
1007	0.742
1008	0
1009	0.938
101	-0.108
1010	0
1011	-0.337
1012	0
1013	-0.0976
1014	-0.0874
1015	0.0647
1016	0.854
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.0487
1022	-0.124
1023	0
1024	-0.307
1025	0
1026	0
1027	-0.048
1028	0
1029	-0.176
103	0
1030	0
1031	0.255
1032	-0.353
1033	-0.0752
1034	0
1035	0
1036	-0.38
1037	0
1038	1.081
1039	-0.026
104	0
1040	1.017
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: CNhs13408

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00278
MA0003.1	MA0003.1	0.927
MA0004.1	MA0004.1	0.357
MA0006.1	MA0006.1	0.269
MA0007.1	MA0007.1	0.93
MA0009.1	MA0009.1	0.578
MA0014.1	MA0014.1	0.85
MA0017.1	MA0017.1	0.124
MA0018.2	MA0018.2	0.0615
MA0019.1	MA0019.1	0.946
MA0024.1	MA0024.1	0.00322
MA0025.1	MA0025.1	0.693
MA0027.1	MA0027.1	0.351
MA0028.1	MA0028.1	1.02974e-6
MA0029.1	MA0029.1	0.983
MA0030.1	MA0030.1	0.665
MA0031.1	MA0031.1	0.72
MA0035.2	MA0035.2	0.131
MA0038.1	MA0038.1	0.00596
MA0039.2	MA0039.2	4.21121e-4
MA0040.1	MA0040.1	0.964
MA0041.1	MA0041.1	0.646
MA0042.1	MA0042.1	0.564
MA0043.1	MA0043.1	0.374
MA0046.1	MA0046.1	3.13162e-5
MA0047.2	MA0047.2	0.985
MA0048.1	MA0048.1	0.0309
MA0050.1	MA0050.1	0.661
MA0051.1	MA0051.1	0.229
MA0052.1	MA0052.1	0.426
MA0055.1	MA0055.1	0.882
MA0057.1	MA0057.1	0.909
MA0058.1	MA0058.1	0.463
MA0059.1	MA0059.1	0.556
MA0060.1	MA0060.1	1.64422e-11
MA0061.1	MA0061.1	0.0658
MA0062.2	MA0062.2	1.96907e-6
MA0065.2	MA0065.2	0.243
MA0066.1	MA0066.1	0.0895
MA0067.1	MA0067.1	0.975
MA0068.1	MA0068.1	0.757
MA0069.1	MA0069.1	0.992
MA0070.1	MA0070.1	0.708
MA0071.1	MA0071.1	0.05
MA0072.1	MA0072.1	0.00447
MA0073.1	MA0073.1	0.526
MA0074.1	MA0074.1	0.284
MA0076.1	MA0076.1	6.13196e-5
MA0077.1	MA0077.1	0.242
MA0078.1	MA0078.1	9.37614e-4
MA0079.2	MA0079.2	0.413
MA0080.2	MA0080.2	0.135
MA0081.1	MA0081.1	0.116
MA0083.1	MA0083.1	3.61076e-4
MA0084.1	MA0084.1	0.778
MA0087.1	MA0087.1	0.804
MA0088.1	MA0088.1	0.655
MA0090.1	MA0090.1	8.76044e-5
MA0091.1	MA0091.1	0.336
MA0092.1	MA0092.1	0.141
MA0093.1	MA0093.1	0.545
MA0099.2	MA0099.2	0.0074
MA0100.1	MA0100.1	0.11
MA0101.1	MA0101.1	0.499
MA0102.2	MA0102.2	0.264
MA0103.1	MA0103.1	1.51952e-4
MA0104.2	MA0104.2	0.103
MA0105.1	MA0105.1	0.658
MA0106.1	MA0106.1	0.00506
MA0107.1	MA0107.1	0.178
MA0108.2	MA0108.2	9.98286e-6
MA0111.1	MA0111.1	0.983
MA0112.2	MA0112.2	0.773
MA0113.1	MA0113.1	0.944
MA0114.1	MA0114.1	0.0287
MA0115.1	MA0115.1	0.449
MA0116.1	MA0116.1	0.308
MA0117.1	MA0117.1	0.115
MA0119.1	MA0119.1	0.0496
MA0122.1	MA0122.1	0.547
MA0124.1	MA0124.1	0.867
MA0125.1	MA0125.1	0.00627
MA0131.1	MA0131.1	0.0391
MA0135.1	MA0135.1	0.273
MA0136.1	MA0136.1	0.0851
MA0137.2	MA0137.2	0.322
MA0138.2	MA0138.2	0.0118
MA0139.1	MA0139.1	0.207
MA0140.1	MA0140.1	0.205
MA0141.1	MA0141.1	0.141
MA0142.1	MA0142.1	0.322
MA0143.1	MA0143.1	0.00637
MA0144.1	MA0144.1	0.405
MA0145.1	MA0145.1	0.425
MA0146.1	MA0146.1	0.263
MA0147.1	MA0147.1	0.0494
MA0148.1	MA0148.1	0.718
MA0149.1	MA0149.1	0.488
MA0150.1	MA0150.1	0.00485
MA0152.1	MA0152.1	0.613
MA0153.1	MA0153.1	9.93577e-5
MA0154.1	MA0154.1	0.204
MA0155.1	MA0155.1	0.688
MA0156.1	MA0156.1	0.0234
MA0157.1	MA0157.1	0.256
MA0159.1	MA0159.1	0.369
MA0160.1	MA0160.1	0.0521
MA0162.1	MA0162.1	0.904
MA0163.1	MA0163.1	0.344
MA0164.1	MA0164.1	0.779
MA0258.1	MA0258.1	0.0809
MA0259.1	MA0259.1	0.59

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: CNhs13408

Novel motif	Logo	P-value
1	1	0.399
10	10	0.857
100	100	0.28
101	101	0.79
102	102	0.359
103	103	0.636
104	104	0.754
105	105	0.129
106	106	0.00402
107	107	0.00199
108	108	0.675
109	109	0.563
11	11	0.34
110	110	0.211
111	111	0.228
112	112	0.299
113	113	0.77
114	114	0.0175
115	115	0.107
116	116	0.978
117	117	0.872
118	118	0.734
119	119	0.855
12	12	0.764
120	120	0.823
121	121	0.617
122	122	0.79
123	123	0.877
124	124	0.282
125	125	0.0194
126	126	0.407
127	127	0.208
128	128	0.0279
129	129	0.0817
13	13	0.431
130	130	0.735
131	131	0.355
132	132	0.426
133	133	0.766
134	134	0.908
135	135	0.306
136	136	0.121
137	137	0.653
138	138	0.427
139	139	0.594
14	14	0.979
140	140	0.688
141	141	0.469
142	142	0.523
143	143	0.0695
144	144	0.0843
145	145	0.11
146	146	0.885
147	147	0.339
148	148	0.493
149	149	0.288
15	15	0.36
150	150	0.0407
151	151	0.432
152	152	0.63
153	153	0.286
154	154	0.369
155	155	0.726
156	156	0.821
157	157	0.637
158	158	0.112
159	159	0.915
160	160	0.909
161	161	0.193
162	162	0.528
163	163	0.654
164	164	0.0924
165	165	0.405
166	166	0.833
167	167	0.576
168	168	0.548
169	169	0.191
17	17	0.131
18	18	0.072
19	19	0.0751
2	2	0.663
20	20	0.357
21	21	0.104
22	22	0.103
23	23	0.0148
24	24	0.915
25	25	0.633
26	26	0.0041
27	27	0.918
28	28	0.753
29	29	0.87
3	3	0.634
30	30	0.689
31	31	0.962
32	32	0.856
33	33	0.593
34	34	0.505
35	35	0.476
36	36	0.204
37	37	0.786
38	38	0.23
39	39	0.49
4	4	0.414
40	40	0.139
41	41	0.0375
42	42	0.492
43	43	0.0912
44	44	0.988
45	45	0.411
46	46	0.0462
47	47	0.707
48	48	0.908
49	49	0.0891
5	5	0.197
50	50	0.879
51	51	0.381
52	52	0.271
53	53	0.654
54	54	0.404
55	55	0.275
56	56	0.587
57	57	0.236
58	58	0.462
59	59	0.073
6	6	0.815
60	60	0.0361
61	61	0.836
62	62	0.206
63	63	0.507
64	64	0.837
65	65	0.389
66	66	0.129
67	67	0.579
68	68	0.156
69	69	0.368
7	7	0.186
70	70	0.0483
71	71	0.176
72	72	0.888
73	73	0.805
74	74	0.982
75	75	0.474
76	76	0.53
77	77	0.338
78	78	0.144
79	79	0.839
8	8	0.694
80	80	0.759
81	81	0.541
82	82	0.16
83	83	0.215
84	84	0.0614
85	85	0.405
86	86	0.6
87	87	0.293
88	88	0.813
89	89	0.705
9	9	0.36
90	90	0.121
91	91	0.272
92	92	0.00628
93	93	6.79852e-5
94	94	0.171
95	95	0.00355
96	96	0.165
97	97	0.0721
98	98	0.953
99	99	0.7

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: CNhs13408

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011508 mouse TSt-4/DLL1 feeder cells 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)
0000066 (epithelial cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002293 (epithelial cell of thymus)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002370 (thymus)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0004177 (hemopoietic organ)
0005057 (immune organ)
0002530 (gland)
0005058 (hemolymphoid system gland)
0010317 (germ layer / neural crest derived structure)
0000153 (anterior region of body)
0002390 (hematopoietic system)
0000949 (endocrine system)
0002193 (hemolymphoid system)
0002405 (immune system)
0009113 (thymic region)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000343 (control treatment sample)
0000350 (experimentally modified sample)
0011508 (mouse TSt-4/DLL1 feeder cells 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:0000223 (endodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005409
+|accession_numbers=CAGE;DRX008909;DRR009783;DRZ001208;DRZ002591;DRZ012558;DRZ013941
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002370,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0004177,UBERON:0005057,UBERON:0002530,UBERON:0005058,UBERON:0010317,UBERON:0000153,UBERON:0002390,UBERON:0000949,UBERON:0002193,UBERON:0002405,UBERON:0009113
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000255,CL:0002076,CL:0002293
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr3:99057269..99057306,+!p1@Tbx15!2.26!216.58!Tbx15;;chr17:44951553..44951586,-!p2@Runx2!2.00!109.57!Runx2;;chr16:14705925..14705951,+!p1@Snai2!1.92!540.19!Snai2;;chr11:44431687..44431706,+!p2@Ebf1!1.77!257.35!Ebf1;;chr16:14705961..14705978,+!p2@Snai2!1.77!254.81!Snai2;;chr1:57029281..57029326,-!p1@Satb2!1.71!76.44!Satb2;;chr1:140739014..140739032,-!p1@Lhx9!1.66!56.06!Lhx9;;chr15:40486566..40486600,+!p1@Zfpm2!1.60!219.13!Zfpm2;;chr16:14705668..14705683,+!p3@Snai2!1.50!30.58!Snai2;;chr11:44430812..44430838,+!p1@Ebf1!1.45!252.26!Ebf1;;chr9:87626083..87626108,-!p1@Tbx18!1.45!58.61!Tbx18;;chr11:96153767..96153822,+!p1@Hoxb6!1.44!40.77!Hoxb6;;chr17:87153028..87153049,+!p2@Epas1!1.42!499.42!Epas1;;chr7:35904304..35904320,+!p1@Cebpa!1.41!479.03!Cebpa;;chr12:34642510..34642530,+!p1@Twist1!1.41!76.44!Twist1;;chr2:30700881..30700916,+!p1@Prrx2!1.41!45.86!Prrx2;;chr11:44431016..44431045,+!p5@Ebf1!1.39!33.12!Ebf1;;chr6:72739034..72739055,-!p3@Tcf7l1!1.38!48.41!Tcf7l1;;chr6:6831950..6831985,-!p2@Dlx5!1.38!25.48!Dlx5;;chr18:35020854..35020869,+!p1@Egr1!1.36!800.09!Egr1;;chr6:6832076..6832092,-!p1@Dlx5!1.36!25.48!Dlx5;;chr7:144506077..144506128,-!p1@Ebf3!1.35!48.41!Ebf3;;chr11:44431710..44431725,+!p7@Ebf1!1.34!33.12!Ebf1;;chr13:99124189..99124205,+!p1@Foxd1!1.33!30.58!Foxd1;;chr15:40486540..40486550,+!p6@Zfpm2!1.33!28.03!Zfpm2;;chr1:57028556..57028583,-!p5@Satb2!1.33!20.38!Satb2;;chr16:14705746..14705761,+!p4@Snai2!1.33!20.38!Snai2;;chr16:92697560..92697592,-!p2@Runx1!1.32!122.31!Runx1;;chr19:28754692..28754757,-!p1@Glis3!1.31!78.99!Glis3;;chr17:87153240..87153254,+!p1@Epas1!1.29!351.63!Epas1;;chr11:44430788..44430804,+!p3@Ebf1!1.29!45.86!Ebf1;;chr17:44872561..44872615,-!p1@Runx2!1.28!40.77!Runx2;;chr12:74147689..74147711,-!p1@Six1!1.27!38.22!Six1;;chr6:115311030..115311065,+!p4@Pparg!1.27!25.48!Pparg;;chr6:52190467..52190500,-!p1@Hoxa10!1.27!17.84!Hoxa10;;chr6:6831986..6832007,-!p4@Dlx5!1.27!17.84!Dlx5;;chr15:102197405..102197454,-!p1@Sp7!1.27!17.84!Sp7;;chr6:72185232..72185272,-!p1@Atoh8!1.26!48.41!Atoh8;;chr19:59533221..59533271,+!p1@Emx2!1.25!20.38!Emx2;;chr13:31898637..31898653,+!p2@Foxc1!1.23!28.03!Foxc1;;chr11:44430877..44430899,+!p6@Ebf1!1.23!20.38!Ebf1;;chr11:98603185..98603208,+!p1@Thra!1.22!909.65!Thra;;chr5:53981692..53981768,+!p2@Rbpj!1.22!272.64!Rbpj;;chr13:31898729..31898761,+!p1@Foxc1!1.22!38.22!Foxc1;;chr3:30408603..30408668,-!p1@Mecom!1.22!35.67!Mecom;;chr15:40486427..40486437,+!p5@Zfpm2!1.22!20.38!Zfpm2;;chr15:102751603..102751630,+!p1@Hoxc13!1.21!15.29!Hoxc13;;chr3:99057256..99057268,+!p3@Tbx15!1.21!15.29!Tbx15;;chr1:57029027..57029056,-!p7@Satb2!1.21!15.29!Satb2;;chr8:94325814..94325839,-!p2@Irx3!1.20!30.58!Irx3;;chr13:31898767..31898785,+!p4@Foxc1!1.19!17.84!Foxc1;;chr19:55816546..55816556,+!p3@Tcf7l2!1.18!53.51!Tcf7l2;;chr11:44430989..44431015,+!p4@Ebf1!1.18!25.48!Ebf1;;chr3:30408674..30408716,-!p2@Mecom!1.18!22.93!Mecom;;chr13:31898496..31898519,+!p3@Foxc1!1.18!22.93!Foxc1;;chr4:97439116..97439202,+!p5@Nfia!1.17!122.31!Nfia;;chr10:119913546..119913583,-!p3@Hmga2!1.16!28.03!Hmga2;;chr6:72185210..72185228,-!p3@Atoh8!1.16!22.93!Atoh8;;chr15:50720601..50720630,-!p2@Trps1!1.14!30.58!Trps1;;chr1:57028538..57028553,-!p6@Satb2!1.14!12.74!Satb2;;chr3:66785181..66785199,-!p2@Shox2!1.14!12.74!Shox2;;chr3:66785201..66785226,-!p3@Shox2!1.14!12.74!Shox2;;chr15:97738692..97738747,-!p1@Vdr!1.13!68.80!Vdr;;chr9:96653241..96653288,-!p1@E030011O05Rik,p5@Zbtb38!1.12!22.93!Zbtb38;;chr6:72185553..72185612,-!p2@Atoh8!1.11!22.93!Atoh8;;chr19:28754600..28754612,-!p2@Glis3!1.08!17.84!Glis3;;chr11:44431626..44431637,+!p10@Ebf1!1.08!12.74!Ebf1;;chr19:26681865..26681900,+!p6@Smarca2!1.06!30.58!Smarca2;;chr6:52163319..52163342,-!p1@Hoxa3!1.06!15.29!Hoxa3;;chr15:101097270..101097290,+!p1@Nr4a1!1.05!107.02!Nr4a1;;chr8:34496298..34496366,+!p1@Purg!1.05!86.63!Purg;;chr15:102828658..102828678,+!p1@Hoxc6!1.05!10.19!Hoxc6;;chr19:26681721..26681746,+!p9@Smarca2!1.04!20.38!Smarca2;;chr1:38684260..38684312,-!p2@Aff3!1.03!68.80!Aff3;;chr11:98603160..98603171,+!p3@Thra!1.03!45.86!Thra;;chr18:75979866..75979890,+!p3@Zbtb7c!1.03!20.38!Zbtb7c;;chr5:107003725..107003746,-!p5@Zfp644!1.03!12.74!Zfp644;;chr12:34642682..34642753,+!p2@Twist1!1.02!25.48!Twist1;;chr15:40486615..40486628,+!p3@Zfpm2!1.02!15.29!Zfpm2;;chr18:14131045..14131062,-!p3@Zfp521!1.02!15.29!Zfp521;;chr9:63869802..63869815,-!p3@Smad6!0.99!17.84!Smad6;;chr17:44873393..44873418,-!p4@Runx2!0.99!15.29!Runx2;;chr10:119913792..119913820,-!p5@Hmga2!0.99!15.29!Hmga2;;chr5:92391466..92391471,+!p2@Thap6!0.99!12.74!Thap6;;chr8:109817400..109817417,+!p1@Nfat5!0.98!183.46!Nfat5;;chr11:112643496..112643562,+!p1@Sox9!0.97!315.96!Sox9;;chr13:55932591..55932622,-!p1@Pitx1!0.97!10.19!Pitx1;;chr5:104121391..104121450,+!p3@Aff1!0.96!43.32!Aff1;;chr19:46380235..46380277,+!p3@Nfkb2!0.96!17.84!Nfkb2;;chr1:92895299..92895373,+!p2@Lrrfip1!0.95!168.17!Lrrfip1;;chr2:167363692..167363710,+!p1@Snai1!0.95!99.37!Snai1;;chr19:26681672..26681716,+!p5@Smarca2!0.94!33.12!Smarca2;;chr2:44972869..44972895,-!p12@Zeb2!0.94!15.29!Zeb2;;chr8:87324311..87324316,-!p8@Nfix!0.94!12.74!Nfix;;chr18:14131020..14131033,-!p4@Zfp521!0.94!10.19!Zfp521;;chr17:44873599..44873623,-!p7@Runx2!0.94!7.64!Runx2;;chr19:5447692..5447711,+!p2@Fosl1!0.94!7.64!Fosl1;;chr16:25684232..25684285,+!p2@Trp63!0.94!7.64!Trp63;;chr17:44951598..44951609,-!p12@Runx2!0.94!7.64!Runx2;;chr1:57029076..57029098,-!p8@Satb2!0.94!7.64!Satb2;;chr1:87497610..87497645,+!p1@Gm2427,p1@Sp140!0.94!7.64!Sp140;;chr4:107107224..107107259,+!p2@Glis1!0.94!7.64!Glis1;;chr4:134676555..134676575,+!p2@Runx3!0.94!7.64!Runx3;;chr6:83661226..83661282,+!p1@Vax2!0.94!7.64!Vax2;;chr17:84587279..84587294,-!p1@Zfp36l2!0.93!830.67!Zfp36l2;;chr17:44873258..44873281,-!p5@Runx2!0.93!10.19!Runx2;;chr11:98798983..98799049,+!p1@Rara!0.92!193.65!Rara;;chr11:97524509..97524595,+!p1@Mllt6!0.92!91.73!Mllt6;;chr6:140572167..140572236,+!p2@Aebp2!0.92!76.44!Aebp2;;chr17:34784073..34784118,+!p2@Atf6b!0.92!30.58!Atf6b;;chr18:7004715..7004731,-!p1@Mkx!0.92!17.84!Mkx;;chr9:63869834..63869849,-!p5@Smad6!0.92!12.74!Smad6;;chr18:64499674..64499696,+!p1@Onecut2!0.91!12.74!Onecut2;;chr18:64499706..64499721,+!p2@Onecut2!0.91!10.19!Onecut2;;chr5:104121453..104121479,+!p4@Aff1!0.90!33.12!Aff1;;chr10:67375368..67375433,-!p1@Zfp365!0.90!12.74!Zfp365;;chr6:115311270..115311298,+!p1@Pparg!0.90!10.19!Pparg;;chr11:44431191..44431205,+!p11@Ebf1!0.90!7.64!Ebf1;;chr15:81633165..81633188,+!p2@Tef!0.89!58.61!Tef;;chr11:102179101..102179130,-!p3@Ubtf!0.89!25.48!Ubtf;;chr2:83484658..83484678,+!p2@Zc3h15!0.88!109.57!Zc3h15;;chr9:68501522..68501538,+!p4@Rora!0.88!12.74!Rora;;chr17:21145981..21145998,+!p2@Zfp160!0.88!12.74!Zfp160;;chr1:165243591..165243625,-!p2@Prrx1!0.88!10.19!Prrx1;;chr3:130813557..130813582,+!p5@Lef1!0.88!7.64!Lef1;;chr15:81641878..81641921,+!p1@Tef!0.87!175.82!Tef;;chr14:65977324..65977372,+!p2@Zfp395!0.87!38.22!Zfp395;;chr15:50721616..50721632,-!p4@Trps1!0.87!17.84!Trps1;;chr9:63869751..63869767,-!p1@Smad6!0.87!17.84!Smad6;;chr15:102300965..102300977,+!p1@Pcbp2!0.86!2117.43!Pcbp2;;chr13:31898529..31898542,+!p5@Foxc1!0.86!7.64!Foxc1;;chr2:38206744..38206766,+!p1@Lhx2!0.86!7.64!Lhx2;;chr4:107107175..107107204,+!p1@Glis1!0.86!7.64!Glis1;;chr7:144505980..144506010,-!p3@Ebf3!0.86!7.64!Ebf3;;chr2:83484681..83484704,+!p1@Zc3h15!0.85!295.57!Zc3h15;;chr6:140571997..140572136,+!p1@Aebp2!0.85!150.34!Aebp2;;chr1:64579555..64579570,+!p3@Creb1!0.85!30.58!Creb1;;chr17:37140628..37140631,+!p2@Zfp57!0.85!12.74!Zfp57;;chr6:52176164..52176195,-!p1@Hoxa9!0.85!7.64!Hoxa9;;chr15:50721588..50721610,-!p1@Trps1!0.84!63.70!Trps1;;chr12:86940338..86940357,+!p1@Jdp2!0.83!61.15!Jdp2;;chr11:44431369..44431389,+!p8@Ebf1!0.83!7.64!Ebf1;;chr8:87502608..87502623,-!p1@Junb!0.82!99.37!Junb;;chr9:96096665..96096699,+!p4@Tfdp2!0.82!20.38!Tfdp2;;chr15:50720589..50720600,-!p12@Trps1!0.82!7.64!Trps1;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.81!15.29!Zfhx3;;chr2:30700857..30700873,+!p3@Prrx2!0.81!7.64!Prrx2;;chr17:21145885..21145977,+!p1@Zfp160!0.80!78.99!Zfp160;;chr10:75495343..75495405,+!p1@Zfp280b!0.80!48.41!Zfp280b;;chr8:118231678..118231692,-!p2@Maf!0.79!50.96!Maf;;chr8:87324292..87324303,-!p4@Nfix!0.79!12.74!Nfix;;chr5:53981592..53981616,+!p3@Rbpj!0.79!10.19!Rbpj;;chr6:6831928..6831949,-!p3@Dlx5!0.79!5.10!Dlx5;;chr6:6813551..6813570,+!p5@Dlx6!0.79!5.10!Dlx6;;chr9:87625971..87625992,-!p2@Tbx18!0.79!5.10!Tbx18;;chr15:102797288..102797302,+!p1@Hoxc10!0.79!5.10!Hoxc10;;chr15:102196790..102196799,-!p3@Sp7!0.79!5.10!Sp7;;chr11:100721640..100721658,+!p2@Stat5a!0.79!5.10!Stat5a;;chr11:44431053..44431060,+!p14@Ebf1!0.79!5.10!Ebf1;;chr11:96132523..96132538,+!p3@Hoxb9!0.79!5.10!Hoxb9;;chr19:5447886..5447905,+!p1@Fosl1!0.79!5.10!Fosl1;;chr19:59532915..59532940,+!p5@Emx2!0.79!5.10!Emx2;;chr1:87497443..87497454,+!p3@Gm2427,p3@Sp140!0.79!5.10!Sp140;;chr1:87546572..87546579,+!p4@Sp100!0.79!5.10!Sp100;;chr2:71367142..71367167,+!p2@Dlx1!0.79!5.10!Dlx1;;chr2:71367871..71367898,+!p1@Dlx1!0.79!5.10!Dlx1;;chr3:54559550..54559570,+!p4@Smad9!0.78!7.64!Smad9;;chr2:44968775..44968795,-!p4@Zeb2!0.77!25.48!Zeb2;;chr10:92773818..92773906,-!p2@Elk3!0.77!25.48!Elk3;;chr16:33380881..33380909,+!p1@Zfp148!0.77!22.93!Zfp148;;chr5:65194853..65194866,+!p5@Klf3!0.77!15.29!Klf3;;chr4:82151583..82151594,-!p6@Nfib!0.77!10.19!Nfib;;chr5:134790507..134790546,-!p1@Gtf2i!0.76!127.40!Gtf2i;;chr17:4994904..4994953,+!p3@Arid1b!0.76!40.77!Arid1b;;chr8:125897750..125897758,+!p2@Tcf25!0.76!35.67!Tcf25;;chr12:112088483..112088512,+!p1@Zfp839!0.76!30.58!Zfp839;;chr9:63869850..63869873,-!p2@Smad6!0.76!15.29!Smad6;;chr2:148506935..148506954,+!p2@Gzf1!0.76!10.19!Gzf1;;chr15:102455867..102455930,-!p1@Atf7!0.75!66.25!Atf7;;chr10:126726055..126726091,-!p2@Mbd6!0.75!40.77!Mbd6;;chr2:83484634..83484647,+!p4@Zc3h15!0.75!35.67!Zc3h15;;chr8:124900576..124900601,+!p2@Zc3h18!0.75!22.93!Zc3h18;;chr16:43363190..43363242,+!p2@Zbtb20!0.75!15.29!Zbtb20;;chr15:81633203..81633215,+!p3@Tef!0.75!7.64!Tef;;chr3:135354384..135354443,-!p1@Nfkb1!0.74!30.58!Nfkb1;;chr10:6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+|ffid_belonging_in_development=CL:0000223
 |fonse_cell_line=FF:0011508
 |fonse_cell_line_closure=FF:0011508
@@ Line 40: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011508
 |is_obsolete=
+|library_id=CNhs13408
+|library_id_phase_based=2:CNhs13408
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12987
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12987
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/TSt-4%252fDLL1%2520feeder%2520cells%252c%2520biol_rep2.CNhs13408.12987-138I8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/TSt-4%252fDLL1%2520feeder%2520cells%252c%2520biol_rep2.CNhs13408.12987-138I8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/TSt-4%252fDLL1%2520feeder%2520cells%252c%2520biol_rep2.CNhs13408.12987-138I8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/TSt-4%252fDLL1%2520feeder%2520cells%252c%2520biol_rep2.CNhs13408.12987-138I8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/TSt-4%252fDLL1%2520feeder%2520cells%252c%2520biol_rep2.CNhs13408.12987-138I8.mm9.nobarcode.rdna.fa.gz
 |name=TSt-4/DLL1 feeder cells, biol_rep2
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13408,LSID1023,release014,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,0.0203354097769631,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0.936722655787531,0,0,0,0,0,0,0,-0.00843276752601008,0,0,0,0,0,-0.209322725495826,-0.0417740847988257,0.0927663973985329,-0.984211366477826,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,-0.0428469550828748,0,0,0,0,0,-0.117389802908326,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,0,0,0,0,0,0,-0.014609338048557,0.189137543326289,-0.0788315948399074,0,0,0,0,0,0,0.269131293823349,-0.332157923972398,0.299194504512442,0,0,0,0,0
 |rna_box=138
 |rna_catalog_number=
@@ Line 58: / Line 74: @@
 |rna_sample_type=
 |rna_tube_id=138I8
-|rna_weight_ug=9.40
+|rna_weight_ug=9.4
 |sample_age=
+|sample_category=time courses
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 95: @@
 |sample_strain=
 |sample_tissue=
+|timecourse=T-cell_differentiation
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12987-138I8;search_select_hide=table117:12987-138I8
 }}

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FF:12987-138I8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:48, 4 June 2020

CNhs13408

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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