FF:13368-143G2: Difference between revisions

Latest revision as of 18:57, 4 June 2020

Name:	Tracheal epithelial cells, differentiation to ciliated epithelial cells
Species:	Mouse (Mus musculus)
Library ID:	CNhs13740
Sample type:	time courses
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	NA
dev stage	NA
sex	female
age	NA
cell type	SELECT CELL TYPE
cell line	NA
company	NA
collaboration	Mitsuru Morimoto
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	0-2
catalog number	NA
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005464

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13740		CAGE		DRX008912		DRR009786

Accession ID Mm9

Library id		BAM		CTSS
CNhs13740		DRZ001211		DRZ002594

Accession ID Mm10

Library id		BAM		CTSS
CNhs13740		DRZ012561		DRZ013944

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

CNhs13740

0	0
1	0
10	0
100	0
1000	0
1001	-0.0668
1002	-0.116
1003	-0.113
1004	0
1005	0.245
1006	-0.378
1007	-0.329
1008	0
1009	-0.0572
101	0.0479
1010	0
1011	-0.2
1012	0
1013	-0.047
1014	0
1015	-0.0623
1016	-0.239
1017	0
1018	0.783
1019	0
102	0
1020	0.178
1021	0.255
1022	-0.0974
1023	0
1024	-0.14
1025	0
1026	0
1027	-0.048
1028	0.246
1029	-0.115
103	-0.0887
1030	0
1031	-0.554
1032	-0.1
1033	0.0144
1034	0
1035	0
1036	0.16
1037	0
1038	-0.22
1039	-0.15
104	0
1040	-0.118
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: CNhs13740

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.368
MA0003.1	MA0003.1	0.435
MA0004.1	MA0004.1	0.808
MA0006.1	MA0006.1	0.267
MA0007.1	MA0007.1	0.459
MA0009.1	MA0009.1	0.184
MA0014.1	MA0014.1	0.0977
MA0017.1	MA0017.1	0.855
MA0018.2	MA0018.2	0.0404
MA0019.1	MA0019.1	0.108
MA0024.1	MA0024.1	0.313
MA0025.1	MA0025.1	0.195
MA0027.1	MA0027.1	0.966
MA0028.1	MA0028.1	4.37321e-6
MA0029.1	MA0029.1	0.444
MA0030.1	MA0030.1	0.94
MA0031.1	MA0031.1	0.989
MA0035.2	MA0035.2	4.87796e-4
MA0038.1	MA0038.1	0.017
MA0039.2	MA0039.2	0.00998
MA0040.1	MA0040.1	0.72
MA0041.1	MA0041.1	0.883
MA0042.1	MA0042.1	0.894
MA0043.1	MA0043.1	0.376
MA0046.1	MA0046.1	5.6182e-5
MA0047.2	MA0047.2	0.0294
MA0048.1	MA0048.1	0.00519
MA0050.1	MA0050.1	0.337
MA0051.1	MA0051.1	0.47
MA0052.1	MA0052.1	0.00988
MA0055.1	MA0055.1	7.31898e-5
MA0057.1	MA0057.1	0.099
MA0058.1	MA0058.1	0.903
MA0059.1	MA0059.1	0.109
MA0060.1	MA0060.1	0.0164
MA0061.1	MA0061.1	0.133
MA0062.2	MA0062.2	2.10292e-8
MA0065.2	MA0065.2	0.235
MA0066.1	MA0066.1	0.313
MA0067.1	MA0067.1	0.327
MA0068.1	MA0068.1	0.966
MA0069.1	MA0069.1	0.36
MA0070.1	MA0070.1	0.0694
MA0071.1	MA0071.1	0.319
MA0072.1	MA0072.1	0.505
MA0073.1	MA0073.1	0.764
MA0074.1	MA0074.1	0.565
MA0076.1	MA0076.1	2.42787e-5
MA0077.1	MA0077.1	0.175
MA0078.1	MA0078.1	0.315
MA0079.2	MA0079.2	0.261
MA0080.2	MA0080.2	0.327
MA0081.1	MA0081.1	0.644
MA0083.1	MA0083.1	0.0508
MA0084.1	MA0084.1	0.361
MA0087.1	MA0087.1	0.342
MA0088.1	MA0088.1	0.168
MA0090.1	MA0090.1	3.72587e-4
MA0091.1	MA0091.1	0.511
MA0092.1	MA0092.1	0.64
MA0093.1	MA0093.1	0.949
MA0099.2	MA0099.2	1.80316e-21
MA0100.1	MA0100.1	0.51
MA0101.1	MA0101.1	3.4387e-4
MA0102.2	MA0102.2	0.34
MA0103.1	MA0103.1	3.54246e-6
MA0104.2	MA0104.2	0.715
MA0105.1	MA0105.1	0.342
MA0106.1	MA0106.1	1.28857e-4
MA0107.1	MA0107.1	0.00655
MA0108.2	MA0108.2	0.533
MA0111.1	MA0111.1	0.575
MA0112.2	MA0112.2	0.00892
MA0113.1	MA0113.1	0.301
MA0114.1	MA0114.1	0.719
MA0115.1	MA0115.1	0.312
MA0116.1	MA0116.1	0.174
MA0117.1	MA0117.1	0.619
MA0119.1	MA0119.1	0.579
MA0122.1	MA0122.1	0.726
MA0124.1	MA0124.1	0.325
MA0125.1	MA0125.1	0.0504
MA0131.1	MA0131.1	0.274
MA0135.1	MA0135.1	0.0789
MA0136.1	MA0136.1	0.00143
MA0137.2	MA0137.2	0.00721
MA0138.2	MA0138.2	0.0176
MA0139.1	MA0139.1	0.575
MA0140.1	MA0140.1	3.63295e-5
MA0141.1	MA0141.1	0.679
MA0142.1	MA0142.1	0.362
MA0143.1	MA0143.1	0.556
MA0144.1	MA0144.1	0.0554
MA0145.1	MA0145.1	0.119
MA0146.1	MA0146.1	0.168
MA0147.1	MA0147.1	0.4
MA0148.1	MA0148.1	0.284
MA0149.1	MA0149.1	0.00584
MA0150.1	MA0150.1	0.00117
MA0152.1	MA0152.1	0.188
MA0153.1	MA0153.1	0.009
MA0154.1	MA0154.1	0.862
MA0155.1	MA0155.1	0.399
MA0156.1	MA0156.1	0.00157
MA0157.1	MA0157.1	0.561
MA0159.1	MA0159.1	4.25351e-4
MA0160.1	MA0160.1	0.932
MA0162.1	MA0162.1	0.321
MA0163.1	MA0163.1	0.0684
MA0164.1	MA0164.1	0.248
MA0258.1	MA0258.1	0.064
MA0259.1	MA0259.1	0.596

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: CNhs13740

Novel motif	Logo	P-value
1	1	0.484
10	10	0.0336
100	100	0.355
101	101	0.0499
102	102	0.264
103	103	0.0565
104	104	0.862
105	105	0.569
106	106	0.128
107	107	0.95
108	108	0.543
109	109	0.0087
11	11	0.284
110	110	0.188
111	111	0.141
112	112	0.914
113	113	0.304
114	114	0.623
115	115	0.749
116	116	0.101
117	117	0.00226
118	118	0.821
119	119	0.308
12	12	0.537
120	120	0.593
121	121	0.992
122	122	0.12
123	123	0.0574
124	124	0.771
125	125	0.0528
126	126	0.884
127	127	0.914
128	128	0.157
129	129	0.681
13	13	5.0794e-7
130	130	0.493
131	131	0.0771
132	132	0.251
133	133	0.0293
134	134	0.188
135	135	0.0601
136	136	0.0097
137	137	0.97
138	138	0.211
139	139	0.184
14	14	0.634
140	140	0.327
141	141	0.329
142	142	0.886
143	143	0.484
144	144	0.234
145	145	0.0302
146	146	0.598
147	147	0.622
148	148	0.639
149	149	0.115
15	15	0.257
150	150	0.329
151	151	0.7
152	152	0.0128
153	153	0.299
154	154	0.306
155	155	0.185
156	156	0.00413
157	157	0.386
158	158	0.532
159	159	0.262
160	160	0.897
161	161	0.726
162	162	0.409
163	163	0.875
164	164	0.0445
165	165	0.18
166	166	0.937
167	167	0.52
168	168	0.323
169	169	0.0472
17	17	0.102
18	18	0.634
19	19	0.743
2	2	0.153
20	20	0.0484
21	21	0.278
22	22	0.539
23	23	0.995
24	24	0.0978
25	25	0.984
26	26	0.011
27	27	0.581
28	28	0.755
29	29	5.91018e-4
3	3	0.106
30	30	0.564
31	31	0.4
32	32	0.142
33	33	0.0655
34	34	0.292
35	35	0.933
36	36	0.0607
37	37	0.0272
38	38	0.761
39	39	0.0693
4	4	0.144
40	40	0.0338
41	41	0.109
42	42	0.409
43	43	0.593
44	44	0.356
45	45	0.898
46	46	0.215
47	47	0.403
48	48	0.424
49	49	0.693
5	5	0.95
50	50	0.58
51	51	0.842
52	52	0.73
53	53	0.168
54	54	0.828
55	55	0.812
56	56	0.838
57	57	0.181
58	58	0.536
59	59	0.757
6	6	0.747
60	60	0.239
61	61	0.111
62	62	0.404
63	63	0.239
64	64	0.654
65	65	0.696
66	66	0.226
67	67	0.196
68	68	0.401
69	69	0.478
7	7	0.211
70	70	0.0181
71	71	0.00884
72	72	0.76
73	73	1.95606e-4
74	74	0.19
75	75	0.0131
76	76	0.244
77	77	0.455
78	78	0.00216
79	79	0.287
8	8	0.264
80	80	0.0301
81	81	0.539
82	82	0.94
83	83	0.585
84	84	0.968
85	85	0.904
86	86	0.268
87	87	0.019
88	88	0.891
89	89	0.861
9	9	0.932
90	90	0.551
91	91	0.325
92	92	0.973
93	93	0.643
94	94	0.298
95	95	0.00109
96	96	0.734
97	97	0.857
98	98	0.258
99	99	0.575

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: CNhs13740

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011232 mouse tracheal ciliated cells differentiation after 0hr 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)
0002202 (epithelial cell of tracheobronchial tree)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002632 (epithelial cell of lower respiratory tract)
0002368 (respiratory epithelial cell)
0000307 (tracheal epithelial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0003126 (trachea)
0002100 (trunk)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0000072 (segment of respiratory tract)
0005177 (trunk region element)
0000464 (anatomical space)
0001005 (respiratory airway)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0007196 (tracheobronchial tree)
0000065 (respiratory tract)
0001558 (lower respiratory tract)
0001004 (respiratory system)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000357 (0 hr sample)
0000645 (tracheal ciliated cell differentiation sample)
0000652 (tracheal ciliated cell line sample)
0011232 (mouse tracheal ciliated cells differentiation after 0hr 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)
CL:0000377 (tracheoblast)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008775
+|DRA_sample_Accession=CAGE@SAMD00005464
+|accession_numbers=CAGE;DRX008912;DRR009786;DRZ001211;DRZ002594;DRZ012561;DRZ013944
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0003126,UBERON:0002100,UBERON:0000064,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0005178,UBERON:0000072,UBERON:0005177,UBERON:0000464,UBERON:0001005,UBERON:0005181,UBERON:0010317,UBERON:0007196,UBERON:0000065,UBERON:0001558,UBERON:0001004,UBERON:0002224,UBERON:0000915
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002202,CL:0000255,CL:0002076,CL:0002632,CL:0002368,CL:0000307
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
+|donor= biol_rep2
 |expression_enrichment_score=chr19:5447886..5447905,+!p1@Fosl1!1.81!63.09!Fosl1;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.80!78.54!Zbtb11;;chr13:31650185..31650201,+!p1@Foxq1!1.70!166.71!Foxq1;;chr12:58646974..58647003,-!p1@Foxa1!1.62!54.47!Foxa1;;chr1:137155026..137155042,-!p1@Elf3!1.53!185.46!Elf3;;chr19:5447692..5447711,+!p2@Fosl1!1.47!28.63!Fosl1;;chr17:27693706..27693724,+!p4@Hmga1,p5@Hmga1-rs1!1.40!58.02!Hmga1;;chr10:119913278..119913298,-!p2@Hmga2!1.39!52.19!Hmga2;;chr2:103143336..103143367,-!p1@Ehf!1.39!37.50!Ehf;;chr3:34548909..34548927,+!p1@Sox2!1.33!34.46!Sox2;;chr14:118636214..118636235,-!p1@Sox21!1.33!24.58!Sox21;;chr13:72766279..72766296,+!p2@Irx2!1.31!28.88!Irx2;;chr13:72101178..72101203,-!p1@Irx1!1.20!23.31!Irx1;;chr8:87502608..87502623,-!p1@Junb!1.19!232.08!Junb;;chr1:194979315..194979359,+!p1@Irf6!1.19!86.90!Irf6;;chr16:92697560..92697592,-!p2@Runx1!1.18!88.42!Runx1;;chr9:96653072..96653154,-!p1@Zbtb38!1.16!35.72!Zbtb38;;chr6:108610766..108610781,+!p2@Bhlhe40!1.16!24.32!Bhlhe40;;chr15:79178060..79178074,+!p2@Maff!1.16!17.74!Maff;;chr16:25801993..25802014,+!p1@Trp63!1.15!13.17!Trp63;;chr5:77543897..77543911,-!p2@Hopx!1.14!24.58!Hopx;;chr10:119913310..119913366,-!p1@Hmga2!1.12!94.50!Hmga2;;chr13:72766250..72766273,+!p1@Irx2!1.09!17.74!Irx2;;chr15:79178013..79178028,+!p3@Maff!1.06!13.93!Maff;;chr14:118636238..118636257,-!p2@Sox21!1.06!10.39!Sox21;;chr8:94881733..94881790,+!p1@Irx5!1.05!20.02!Irx5;;chr15:79177964..79177986,+!p1@Maff!1.03!33.70!Maff;;chr15:79178029..79178044,+!p4@Maff!1.03!11.91!Maff;;chr15:37162834..37162849,+!p2@Grhl2!1.03!11.65!Grhl2;;chr11:21901608..21901634,-!p1@Otx1!1.03!9.63!Otx1;;chr1:193007123..193007139,-!p1@Atf3!1.02!53.21!Atf3;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.95!11.40!Carhsp1;;chr6:52141694..52141715,-!p1@Hoxa4!0.95!10.13!Hoxa4;;chr11:21901587..21901604,-!p2@Otx1!0.95!7.85!Otx1;;chr12:57796615..57796687,+!p1@Pax9!0.95!7.85!Pax9;;chr1:194979361..194979373,+!p2@Irf6!0.94!10.64!Irf6;;chr2:30700881..30700916,+!p1@Prrx2!0.93!14.44!Prrx2;;chr17:71200415..71200427,-!p5@Tgif1!0.93!12.41!Tgif1;;chr12:74147689..74147711,-!p1@Six1!0.92!16.47!Six1;;chr19:25746898..25746910,+!p1@Dmrt2!0.92!11.15!Dmrt2;;chr13:72101161..72101177,-!p2@Irx1!0.90!9.88!Irx1;;chr2:30700788..30700824,+!p2@Prrx2!0.89!10.64!Prrx2;;chr14:118635860..118635885,-!p3@Sox21!0.89!6.84!Sox21;;chr6:128250471..128250519,-!p1@Tead4!0.88!13.68!Tead4;;chr13:72101141..72101158,-!p3@Irx1!0.88!8.36!Irx1;;chr2:103143315..103143328,-!p2@Ehf!0.87!6.33!Ehf;;chr6:52154386..52154407,-!p2@Hoxa5!0.84!7.60!Hoxa5;;chr16:55966451..55966484,+!p3@Rpl24,p3@Zbtb11!0.83!35.98!Zbtb11;;chr4:109650609..109650653,+!p1@Dmrta2!0.82!5.57!Dmrta2;;chr8:77540128..77540145,+!p2@Hmgxb4!0.82!5.57!Hmgxb4;;chr10:119913266..119913277,-!p6@Hmga2!0.82!5.57!Hmga2;;chr11:69468531..69468557,+!p1@Sox15!0.82!5.57!Sox15;;chr17:27693746..27693759,+!p6@Hmga1-rs1,p7@Hmga1!0.81!11.40!Hmga1;;chr8:94325814..94325839,-!p2@Irx3!0.79!11.40!Irx3;;chrX:48559194..48559210,-!p4@Mbnl3!0.79!6.59!Mbnl3;;chr15:101097270..101097290,+!p1@Nr4a1!0.78!56.25!Nr4a1;;chr19:46379199..46379301,+!p1@Nfkb2!0.78!31.42!Nfkb2;;chr2:30700857..30700873,+!p3@Prrx2!0.78!7.09!Prrx2;;chr3:34548946..34548972,+!p2@Sox2!0.78!5.57!Sox2;;chr11:116196664..116196679,-!p1@Foxj1!0.77!7.85!Foxj1;;chr6:52154414..52154462,-!p1@Hoxa5!0.76!6.84!Hoxa5;;chr16:18587076..18587106,-!p1@Tbx1!0.75!6.84!Tbx1;;chr14:99697871..99697934,+!p1@Klf5!0.74!99.82!Klf5;;chr1:36364590..36364608,+!p1@Arid5a!0.74!50.67!Arid5a;;chr13:5860776..5860796,+!p1@Klf6!0.73!119.08!Klf6;;chr7:20214704..20214800,-!p1@Relb!0.73!15.71!Relb;;chr15:35225845..35225867,+!p1@Osr2!0.72!11.65!Osr2;;chr8:94325321..94325366,-!p1@Irx3!0.72!11.15!Irx3;;chr13:5860872..5860883,+!p3@Klf6!0.72!9.12!Klf6;;chr17:86087592..86087615,-!p1@Six2!0.72!4.31!Six2;;chr6:51382677..51382783,+!p1@Nfe2l3!0.71!11.65!Nfe2l3;;chr15:37162796..37162828,+!p1@Grhl2!0.71!7.35!Grhl2;;chr12:57636240..57636256,-!p4@Nkx2-1!0.70!4.05!Nkx2-1;;chr1:69732511..69732540,-!p2@Ikzf2!0.69!5.32!Ikzf2;;chr6:108610610..108610676,+!p1@Bhlhe40!0.68!214.60!Bhlhe40;;chr17:71200529..71200556,-!p1@Tgif1!0.68!69.42!Tgif1;;chr19:5637528..5637548,+!p2@Rela!0.68!25.08!Rela;;chr11:101646566..101646603,-!p1@Etv4!0.68!13.68!Etv4;;chr5:32438395..32438406,+!p3@Fosl2!0.68!6.08!Fosl2;;chr11:83664365..83664383,+!p1@Hnf1b!0.68!3.80!Hnf1b;;chr1:194979383..194979393,+!p3@Irf6!0.68!3.80!Irf6;;chr15:61817095..61817111,+!p1@Myc!0.67!250.83!Myc;;chr16:92697354..92697362,-!p3@Runx1!0.67!6.08!Runx1;;chr6:52114821..52114828,-!p1@Hoxa2!0.67!5.83!Hoxa2;;chr6:128250380..128250442,-!p2@Tead4!0.67!4.81!Tead4;;chr6:29490887..29490891,+!p5@Irf5!0.67!4.56!Irf5;;chr17:27693788..27693803,+!p3@Hmga1,p4@Hmga1-rs1!0.66!18.24!Hmga1;;chr17:48025139..48025166,-!p8@Foxp4!0.66!4.31!Foxp4;;chr13:40826961..40827001,-!p4@Tfap2a!0.66!3.55!Tfap2a;;chr13:40825465..40825469,-!p2@Tfap2a!0.66!3.55!Tfap2a;;chr5:92391466..92391471,+!p2@Thap6!0.65!5.32!Thap6;;chr8:124984566..124984595,-!p1@Snai3!0.64!5.57!Snai3;;chr14:17407878..17407926,-!p1@Rarb!0.63!8.11!Rarb;;chr7:20162663..20162678,+!p1@Zfp296!0.63!4.56!Zfp296;;chr12:57636034..57636087,-!p1@Nkx2-1!0.63!3.29!Nkx2-1;;chr15:80085920..80085941,+!p1@Atf4!0.61!428.68!Atf4;;chr3:135354384..135354443,-!p1@Nfkb1!0.61!22.55!Nfkb1;;chrX:7339938..7339963,+!p1@Tfe3!0.61!18.24!Tfe3;;chr19:28754692..28754757,-!p1@Glis3!0.61!14.95!Glis3;;chr8:94325486..94325510,-!p4@Irx3!0.61!4.31!Irx3;;chr12:57636178..57636194,-!p2@Nkx2-1!0.61!3.04!Nkx2-1;;chr8:73905344..73905381,-!p2@Nr2f6!0.60!8.11!Nr2f6;;chr17:45692676..45692695,+!p2@Nfkbie!0.60!6.84!Nfkbie;;chr13:31898496..31898519,+!p3@Foxc1!0.60!5.32!Foxc1;;chr19:5560600..5560617,-!p1@Ovol1!0.60!3.80!Ovol1;;chr14:17407970..17408015,-!p2@Rarb!0.59!8.87!Rarb;;chr17:32506357..32506377,-!p3@Wiz!0.59!6.84!Wiz;;chr6:146744595..146744613,+!p2@Arntl2!0.59!5.32!Arntl2;;chr16:55966407..55966447,+!p6@Rpl24,p6@Zbtb11!0.58!7.85!Zbtb11;;chr6:146744563..146744594,+!p1@Arntl2!0.58!5.83!Arntl2;;chr8:94881686..94881700,+!p4@Irx5!0.58!2.79!Irx5;;chr14:118636183..118636192,-!p4@Sox21!0.58!2.79!Sox21;;chr12:58647114..58647128,-!p2@Foxa1!0.58!2.79!Foxa1;;chr3:98186461..98186476,+!p2@Zfp697!0.58!2.79!Zfp697;;chr9:63605740..63605771,-!p1@Smad3!0.57!48.65!Smad3;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.57!12.92!Ppp1r13l;;chr3:30993974..30994045,+!p1@Skil!0.56!92.22!Skil;;chr18:3281034..3281104,-!p1@Crem!0.56!22.80!Crem;;chr10:119913546..119913583,-!p3@Hmga2!0.56!6.33!Hmga2;;chr4:124805061..124805087,-!p1@Zc3h12a!0.55!9.37!Zc3h12a;;chr15:102087880..102087927,-!p2@Rarg!0.55!6.84!Rarg;;chr11:120624106..120624107,+!p13@Hmga1-rs1,p14@Hmga1!0.55!2.53!Hmga1;;chr12:36219645..36219730,-!p1@Ahr!0.54!30.91!Ahr;;chr1:135551736..135551746,-!p3@Zc3h11a!0.53!4.05!Zc3h11a;;chr6:128250521..128250543,-!p3@Tead4!0.52!4.05!Tead4;;chr11:96180045..96180059,+!p1@Hoxb4!0.52!3.55!Hoxb4;;chr8:94325779..94325791,-!p7@Irx3!0.52!2.28!Irx3;;chr19:5447859..5447866,+!p3@Fosl1!0.52!2.28!Fosl1;;chr5:32438831..32438878,+!p1@Fosl2!0.51!30.15!Fosl2;;chr13:31650026..31650045,+!p2@Foxq1!0.51!4.31!Foxq1;;chr8:94325847..94325869,-!p3@Irx3!0.51!4.05!Irx3;;chr11:101646480..101646496,-!p4@Etv4!0.51!3.04!Etv4;;chr13:31898529..31898542,+!p5@Foxc1!0.50!2.79!Foxc1;;chr12:86814833..86814846,+!p1@Fos!0.49!65.37!Fos;;chr11:59285934..59285962,-!p1@Zfp867!0.49!9.88!Zfp867;;chr5:107003725..107003746,-!p5@Zfp644!0.49!3.04!Zfp644;;chr3:30995296..30995300,+!p6@Skil!0.49!2.79!Skil;;chr7:133839456..133839523,+!p1@Bola2!0.48!136.56!Bola2;;chr11:120624132..120624143,+!p10@Hmga1,p9@Hmga1-rs1!0.48!2.79!Hmga1;;chr10:119913954..119913972,-!p8@Hmga2!0.48!2.03!Hmga2;;chr17:37139555..37139562,+!p6@Zfp57!0.48!2.03!Zfp57;;chr5:77543935..77543947,-!p4@Hopx!0.48!2.03!Hopx;;chr15:37163124..37163153,+!p3@Grhl2!0.48!2.03!Grhl2;;chr4:149611311..149611317,+!p2@Eno1!0.47!7.35!Eno1;;chrX:34443339..34443348,-!p2@Nkrf!0.47!6.59!Nkrf;;chr17:21626055..21626081,+!p2@Zfp53!0.47!3.80!Zfp53;;chr1:92949999..92950097,+!p1@Lrrfip1!0.46!69.93!Lrrfip1;;chr18:84255841..84255883,-!p1@Tshz1!0.46!17.74!Tshz1;;chr10:119913792..119913820,-!p5@Hmga2!0.46!3.80!Hmga2;;chr8:94325273..94325288,-!p5@Irx3!0.46!2.53!Irx3;;chr2:75542527..75542590,-!p1@Nfe2l2!0.45!227.01!Nfe2l2;;chr11:98636531..98636559,-!p1@Nr1d1!0.45!14.19!Nr1d1;;chr19:5637489..5637500,+!p5@Rela!0.45!5.83!Rela;;chr5:147760216..147760292,+!p1@Gtf3a!0.44!113.00!Gtf3a;;chr6:53523358..53523388,+!p1@Creb5!0.44!29.64!Creb5;;chr4:133801453..133801492,-!p1@Zfp593!0.44!20.02!Zfp593;;chr7:77511234..77511302,-!p2@Nr2f2!0.44!15.96!Nr2f2;;chr19:5637501..5637517,+!p4@Rela!0.44!9.63!Rela;;chr9:31720843..31720888,-!p1@Barx2!0.44!2.03!Barx2;;chr8:77540157..77540170,+!p3@Hmgxb4!0.44!1.77!Hmgxb4;;chr8:87502350..87502362,-!p2@Junb!0.44!1.77!Junb;;chr11:69468501..69468515,+!p2@Sox15!0.44!1.77!Sox15;;chr13:40824310..40824314,-!p6@Tfap2a!0.44!1.77!Tfap2a;;chr12:57636220..57636236,-!p3@Nkx2-1!0.44!1.77!Nkx2-1;;chr2:103264213..103264233,+!p1@Elf5!0.44!1.77!Elf5;;chr2:147871627..147871641,-!p1@Foxa2!0.44!1.77!Foxa2;;chr1:69732797..69732812,-!p5@Ikzf2!0.44!1.77!Ikzf2;;chrX:48499591..48499593,-!p3@Mbnl3!0.44!1.77!Mbnl3;;chr4:133801494..133801519,-!p2@Zfp593!0.43!16.47!Zfp593;;chr13:117099847..117099907,-!p1@Isl1!0.43!3.80!Isl1;;chr11:121380594..121380609,-!p2@Zfp750!0.43!3.55!Zfp750;;chr11:121380640..121380655,-!p1@Zfp750!0.43!3.29!Zfp750;;chr14:79915502..79915514,+!p4@Elf1!0.43!3.04!Elf1;;chr15:61816932..61816952,+!p2@Myc!0.42!19.26!Myc;;chr5:32438894..32438908,+!p2@Fosl2!0.42!4.31!Fosl2;;chr3:32264530..32264544,-!p2@Zmat3!0.42!3.04!Zmat3;;chr16:30065419..30065437,+!p1@Hes1!0.41!124.15!Hes1;;chr16:17531086..17531109,-!p3@Thap7!0.41!6.59!Thap7;;chr10:107769719..107769745,+!p4@Pawr!0.41!2.79!Pawr;;chr18:11052606..11052633,+!p4@Gata6!0.40!5.07!Gata6;;chr13:40826150..40826167,-!p3@Tfap2a!0.40!1.77!Tfap2a;;chr13:72766234..72766243,+!p3@Irx2!0.40!1.52!Irx2;;chr8:94881639..94881650,+!p5@Irx5!0.40!1.52!Irx5;;chr2:30700830..30700843,+!p4@Prrx2!0.40!1.52!Prrx2;;chr7:20408047..20408125,-!p1@Bcl3!0.39!24.58!Bcl3;;chr10:107769168..107769215,+!p1@Pawr!0.39!2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 |ffid_belonging_in_development=CL:0000223,CL:0000377
@@ Line 42: / Line 45: @@
 |is_a=EFO:0002091;;FF:0011232
 |is_obsolete=
-|library_ids=CNhs13740
+|library_id=CNhs13740
-|name=Tracheal epithelial cells, differentiation to ciliated epithelial cells, 000hr, biol_rep2
+|library_id_phase_based=2:CNhs13740
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;13368
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;13368
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep2.CNhs13740.13368-143G2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep2.CNhs13740.13368-143G2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep2.CNhs13740.13368-143G2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep2.CNhs13740.13368-143G2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep2.CNhs13740.13368-143G2.mm9.nobarcode.rdna.fa.gz
+|name=Tracheal epithelial cells, differentiation to ciliated epithelial cells
 |namespace=
 |part_of=
@@ Line 83: / Line 96: @@
 |sample_strain=C57BL/6J
 |sample_tissue=
+|time= 000hr
+|timecourse=Tracheal_to_ciliated_epithelium
 |top_motifs=
 |xref=
-}} {{DRAAccessionNumbers
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:13368-143G2;search_select_hide=table117:13368-143G2
-|DRA_sample_Accession=CAGE@DRS008775
-|accession_numbers=DRX008912;DRR009786;DRZ001211;DRZ002594;CAGE
-|library_id=CNhs13740
 }}

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FF:13368-143G2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:57, 4 June 2020

CNhs13740

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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