FF:11743-123F6: Difference between revisions

Latest revision as of 18:17, 4 June 2020

Name:	Mouse Neurons - ventral spinal cord, donor2
Species:	Mouse (Mus musculus)
Library ID:	CNhs12638
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	spinal cord
dev stage	NA
sex	NA
age	NA
cell type	neuron
cell line	NA
company	Sciencell/3H
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	RNASPI2
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005914

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12638		CAGE		DRX008850		DRR009722

Accession ID Mm9

Library id		BAM		CTSS
CNhs12638		DRZ001147		DRZ002532

Accession ID Mm10

Library id		BAM		CTSS
CNhs12638		DRZ012497		DRZ013882

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

CNhs12638

0	0
1	0.601
10	0
100	0.154
1000	0.0189
1001	-0.0668
1002	0.099
1003	0.157
1004	0
1005	0
1006	0.497
1007	-0.148
1008	0
1009	-0.0912
101	-0.0689
1010	0
1011	0.233
1012	0.0578
1013	0.116
1014	0.111
1015	0.213
1016	0.23
1017	0
1018	0
1019	0
102	0
1020	0.569
1021	0.106
1022	0.0305
1023	0
1024	0.0247
1025	0.0933
1026	0
1027	0.384
1028	0
1029	-0.0672
103	0.0578
1030	0
1031	-0.115
1032	0.281
1033	0
1034	0
1035	0.109
1036	-0.135
1037	0
1038	0.0523
1039	-0.0181
104	0
1040	-0.242
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: CNhs12638

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	1.03738e-4
MA0003.1	MA0003.1	0.272
MA0004.1	MA0004.1	0.398
MA0006.1	MA0006.1	0.169
MA0007.1	MA0007.1	0.178
MA0009.1	MA0009.1	0.635
MA0014.1	MA0014.1	0.515
MA0017.1	MA0017.1	6.6315e-7
MA0018.2	MA0018.2	0.153
MA0019.1	MA0019.1	0.529
MA0024.1	MA0024.1	0.772
MA0025.1	MA0025.1	0.584
MA0027.1	MA0027.1	0.255
MA0028.1	MA0028.1	0.0752
MA0029.1	MA0029.1	0.898
MA0030.1	MA0030.1	0.212
MA0031.1	MA0031.1	0.00795
MA0035.2	MA0035.2	0.00554
MA0038.1	MA0038.1	0.281
MA0039.2	MA0039.2	0.0344
MA0040.1	MA0040.1	0.244
MA0041.1	MA0041.1	0.23
MA0042.1	MA0042.1	0.614
MA0043.1	MA0043.1	0.654
MA0046.1	MA0046.1	1.43442e-13
MA0047.2	MA0047.2	8.2378e-7
MA0048.1	MA0048.1	0.13
MA0050.1	MA0050.1	8.60437e-6
MA0051.1	MA0051.1	2.07095e-4
MA0052.1	MA0052.1	0.105
MA0055.1	MA0055.1	0.0684
MA0057.1	MA0057.1	0.269
MA0058.1	MA0058.1	0.38
MA0059.1	MA0059.1	0.189
MA0060.1	MA0060.1	0.126
MA0061.1	MA0061.1	0.0829
MA0062.2	MA0062.2	5.57477e-4
MA0065.2	MA0065.2	2.75961e-6
MA0066.1	MA0066.1	0.0505
MA0067.1	MA0067.1	0.715
MA0068.1	MA0068.1	0.561
MA0069.1	MA0069.1	0.121
MA0070.1	MA0070.1	0.399
MA0071.1	MA0071.1	0.0621
MA0072.1	MA0072.1	0.047
MA0073.1	MA0073.1	0.991
MA0074.1	MA0074.1	0.126
MA0076.1	MA0076.1	0.164
MA0077.1	MA0077.1	0.315
MA0078.1	MA0078.1	0.72
MA0079.2	MA0079.2	0.385
MA0080.2	MA0080.2	1.2721e-10
MA0081.1	MA0081.1	0.272
MA0083.1	MA0083.1	0.149
MA0084.1	MA0084.1	0.578
MA0087.1	MA0087.1	0.299
MA0088.1	MA0088.1	0.171
MA0090.1	MA0090.1	0.0819
MA0091.1	MA0091.1	0.233
MA0092.1	MA0092.1	0.202
MA0093.1	MA0093.1	0.435
MA0099.2	MA0099.2	1.03833e-4
MA0100.1	MA0100.1	0.273
MA0101.1	MA0101.1	0.0486
MA0102.2	MA0102.2	0.64
MA0103.1	MA0103.1	0.0842
MA0104.2	MA0104.2	0.876
MA0105.1	MA0105.1	0.0525
MA0106.1	MA0106.1	0.089
MA0107.1	MA0107.1	0.0883
MA0108.2	MA0108.2	0.0602
MA0111.1	MA0111.1	0.94
MA0112.2	MA0112.2	1.78424e-4
MA0113.1	MA0113.1	0.131
MA0114.1	MA0114.1	7.52876e-6
MA0115.1	MA0115.1	6.38204e-5
MA0116.1	MA0116.1	0.0879
MA0117.1	MA0117.1	0.628
MA0119.1	MA0119.1	0.125
MA0122.1	MA0122.1	0.979
MA0124.1	MA0124.1	0.941
MA0125.1	MA0125.1	0.205
MA0131.1	MA0131.1	0.886
MA0135.1	MA0135.1	0.997
MA0136.1	MA0136.1	2.39575e-13
MA0137.2	MA0137.2	0.15
MA0138.2	MA0138.2	0.0277
MA0139.1	MA0139.1	0.418
MA0140.1	MA0140.1	2.5467e-4
MA0141.1	MA0141.1	0.00361
MA0142.1	MA0142.1	0.325
MA0143.1	MA0143.1	0.667
MA0144.1	MA0144.1	0.0619
MA0145.1	MA0145.1	0.0443
MA0146.1	MA0146.1	0.0165
MA0147.1	MA0147.1	0.718
MA0148.1	MA0148.1	7.50798e-7
MA0149.1	MA0149.1	0.0587
MA0150.1	MA0150.1	0.0146
MA0152.1	MA0152.1	0.0504
MA0153.1	MA0153.1	2.5904e-13
MA0154.1	MA0154.1	0.0325
MA0155.1	MA0155.1	0.713
MA0156.1	MA0156.1	1.28954e-8
MA0157.1	MA0157.1	0.0158
MA0159.1	MA0159.1	0.00183
MA0160.1	MA0160.1	0.0164
MA0162.1	MA0162.1	0.277
MA0163.1	MA0163.1	9.28277e-4
MA0164.1	MA0164.1	0.961
MA0258.1	MA0258.1	0.00775
MA0259.1	MA0259.1	0.975

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: CNhs12638

Novel motif	Logo	P-value
1	1	0.133
10	10	0.0782
100	100	0.604
101	101	0.792
102	102	0.951
103	103	0.0727
104	104	0.609
105	105	0.22
106	106	0.0383
107	107	0.124
108	108	0.412
109	109	0.00653
11	11	0.0645
110	110	0.0474
111	111	0.0573
112	112	0.00279
113	113	0.838
114	114	0.105
115	115	0.754
116	116	0.694
117	117	0.00687
118	118	0.294
119	119	0.0836
12	12	0.966
120	120	0.322
121	121	0.0805
122	122	0.555
123	123	0.0126
124	124	0.248
125	125	0.552
126	126	0.0575
127	127	0.0792
128	128	0.0319
129	129	0.118
13	13	7.75192e-6
130	130	0.23
131	131	0.535
132	132	0.767
133	133	0.994
134	134	0.356
135	135	0.301
136	136	0.123
137	137	0.733
138	138	0.91
139	139	0.167
14	14	0.762
140	140	0.152
141	141	0.381
142	142	0.481
143	143	0.409
144	144	0.875
145	145	0.00283
146	146	0.249
147	147	0.511
148	148	0.534
149	149	0.35
15	15	0.0882
150	150	0.099
151	151	0.441
152	152	0.0788
153	153	0.387
154	154	0.788
155	155	0.489
156	156	8.79606e-5
157	157	0.278
158	158	0.025
159	159	0.0538
160	160	0.263
161	161	0.132
162	162	0.826
163	163	0.307
164	164	0.0132
165	165	0.0606
166	166	0.921
167	167	0.59
168	168	0.786
169	169	0.00183
17	17	0.032
18	18	0.965
19	19	0.122
2	2	0.906
20	20	0.105
21	21	0.378
22	22	0.114
23	23	0.448
24	24	0.0318
25	25	0.66
26	26	1.0795e-6
27	27	0.715
28	28	0.537
29	29	0.0527
3	3	0.0673
30	30	0.959
31	31	0.933
32	32	0.794
33	33	0.102
34	34	0.739
35	35	0.984
36	36	0.339
37	37	0.0244
38	38	0.358
39	39	0.381
4	4	0.441
40	40	0.252
41	41	0.313
42	42	0.17
43	43	0.115
44	44	0.774
45	45	0.594
46	46	0.053
47	47	0.197
48	48	0.123
49	49	0.12
5	5	0.111
50	50	0.31
51	51	0.651
52	52	0.331
53	53	0.898
54	54	0.762
55	55	0.952
56	56	0.449
57	57	0.633
58	58	0.226
59	59	0.112
6	6	0.921
60	60	0.0343
61	61	0.0935
62	62	0.101
63	63	0.113
64	64	0.591
65	65	0.225
66	66	0.739
67	67	0.695
68	68	0.507
69	69	0.375
7	7	0.0215
70	70	0.0141
71	71	0.00954
72	72	0.532
73	73	0.0234
74	74	0.772
75	75	0.0488
76	76	0.518
77	77	0.355
78	78	0.0111
79	79	0.29
8	8	0.0802
80	80	0.606
81	81	0.937
82	82	0.234
83	83	0.057
84	84	0.512
85	85	0.0856
86	86	0.156
87	87	0.26
88	88	0.213
89	89	0.245
9	9	0.373
90	90	0.0848
91	91	0.275
92	92	0.359
93	93	0.0222
94	94	0.689
95	95	0.0384
96	96	0.155
97	97	0.922
98	98	0.404
99	99	0.609

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: CNhs12638

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000207 mouse neuron of the ventral spinal cord 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)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002612 (neuron of the ventral spinal cord)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002240 (spinal cord)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0000489 (cavitated compound organ)
0005174 (dorsal region element)
0001948 (regional part of spinal cord)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002257 (ventral horn of spinal cord)
0001016 (nervous system)
0001137 (dorsum)
0002315 (gray matter of spinal cord)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000207 (mouse neuron of the ventral spinal cord 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:0000133 (neurectodermal cell)
CL:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008740
+|DRA_sample_Accession=CAGE@SAMD00005914
+|accession_numbers=CAGE;DRX008850;DRR009722;DRZ001147;DRZ002532;DRZ012497;DRZ013882
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002240,UBERON:0004121,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0000489,UBERON:0005174,UBERON:0001948,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0002257,UBERON:0001016,UBERON:0001137,UBERON:0002315
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000117,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0002612
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:96143666..96143725,+!p1@Hoxb8!2.33!242.03!Hoxb8;;chr16:91270004..91270023,+!p1@Olig1!2.31!229.08!Olig1;;chr2:74529970..74529997,+!p1@Hoxd10!1.89!75.74!Hoxd10;;chr9:91260594..91260612,-!p1@Zic1!1.81!63.64!Zic1;;chr16:91225808..91225824,+!p1@Olig2!1.74!53.67!Olig2;;chr11:96143962..96144035,+!p2@Hoxb8!1.73!52.96!Hoxb8;;chr3:95032091..95032183,-!p1@Mllt11!1.72!418.00!Mllt11;;chr5:138199361..138199441,+!p2@Tsc22d4!1.72!95.39!Tsc22d4;;chr9:91260616..91260653,-!p2@Zic1!1.62!41.15!Zic1;;chr14:33412570..33412586,+!p1@Prrxl1!1.62!40.29!Prrxl1;;chr2:74550015..74550057,+!p2@Hoxd3!1.60!38.58!Hoxd3;;chr12:54349410..54349461,+!p1@Npas3!1.59!44.99!Npas3;;chr6:52190467..52190500,-!p1@Hoxa10!1.57!36.45!Hoxa10;;chr19:19185671..19185693,-!p1@Rorb!1.52!75.74!Rorb;;chr15:102797288..102797302,+!p1@Hoxc10!1.51!31.32!Hoxc10;;chr7:116154364..116154444,+!p1@Tub!1.50!52.11!Tub;;chr11:96147952..96147967,+!p1@Hoxb7!1.50!37.59!Hoxb7;;chr17:48015839..48015915,-!p3@Foxp4!1.49!35.17!Foxp4;;chr11:96143843..96143868,+!p3@Hoxb8!1.48!29.19!Hoxb8;;chr6:52176164..52176195,-!p1@Hoxa9!1.46!34.03!Hoxa9;;chr12:30219426..30219506,+!p2@Myt1l!1.43!25.91!Myt1l;;chr10:84218895..84218909,+!p1@Rfx4!1.41!24.63!Rfx4;;chr4:150482563..150482655,-!p2@Camta1!1.40!84.14!Camta1;;chr2:65683890..65683907,+!p1@Csrnp3!1.40!45.27!Csrnp3;;chr11:84339016..84339044,-!p1@Lhx1!1.39!23.78!Lhx1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.38!29.19!Pou3f3;;chr6:55631042..55631102,-!p1@Neurod6!1.38!23.06!Neurod6;;chr15:102767247..102767265,+!p1@Hoxc12!1.38!22.78!Hoxc12;;chr3:34548909..34548927,+!p1@Sox2!1.37!37.16!Sox2;;chr11:44431016..44431045,+!p5@Ebf1!1.37!31.32!Ebf1;;chr6:52184901..52184959,-!p2@Hoxa10!1.37!22.21!Hoxa10;;chr14:104867201..104867258,-!p1@Pou4f1!1.34!29.47!Pou4f1;;chr11:96153767..96153822,+!p1@Hoxb6!1.31!29.90!Hoxb6;;chr11:96160360..96160397,+!p3@Hoxb6!1.30!19.08!Hoxb6;;chr16:91270091..91270143,+!p2@Olig1!1.29!18.51!Olig1;;chrX:34442872..34442899,-!p1@Nkrf!1.28!23.35!Nkrf;;chr17:25707623..25707639,-!p1@Sox8!1.26!71.61!Sox8;;chr2:74549968..74549996,+!p1@Hoxd3!1.26!21.50!Hoxd3;;chr4:154335024..154335039,+!p1@Hes5!1.26!20.64!Hes5;;chr7:144505980..144506010,-!p3@Ebf3!1.26!20.64!Ebf3;;chr3:34548946..34548972,+!p2@Sox2!1.26!18.94!Sox2;;chr12:30213247..30213333,+!p1@Myt1l!1.26!17.08!Myt1l;;chr7:30088977..30089002,+!p2@Dpf1!1.25!22.92!Dpf1;;chr2:74529998..74530020,+!p2@Hoxd10!1.24!16.37!Hoxd10;;chr15:76352677..76352737,-!p3@Scrt1!1.24!16.23!Scrt1;;chr15:102797225..102797243,+!p2@Hoxc10!1.23!15.80!Hoxc10;;chr7:144505957..144505972,-!p2@Ebf3!1.22!19.22!Ebf3;;chr11:96143728..96143745,+!p4@Hoxb8!1.20!14.81!Hoxb8;;chr11:96160426..96160443,+!p2@Hoxb6!1.19!14.52!Hoxb6;;chr1:189821714..189821761,+!p1@Esrrg!1.18!26.05!Esrrg;;chr3:95032197..95032208,-!p3@Mllt11!1.18!17.65!Mllt11;;chr7:148008023..148008092,-!p1@Zfp941!1.17!33.46!Zfp941;;chr11:44430989..44431015,+!p4@Ebf1!1.15!23.35!Ebf1;;chr1:19199236..19199258,+!p1@Tfap2b!1.15!13.24!Tfap2b;;chr2:74517742..74517758,+!p2@Hoxd11!1.14!12.96!Hoxd11;;chr5:98609885..98609900,+!p1@Prdm8!1.14!12.81!Prdm8;;chr7:25292331..25292421,+!p1@Zfp428!1.13!88.98!Zfp428;;chr15:78994907..78994926,-!p1@Sox10!1.13!32.03!Sox10;;chr8:24780125..24780143,+!p1@Zmat4!1.13!17.94!Zmat4;;chr11:98190918..98190951,-!p1@Neurod2!1.13!12.53!Neurod2;;chr11:23978291..23978323,+!p7@Bcl11a!1.12!12.24!Bcl11a;;chr11:96132767..96132796,+!p2@Hoxb9!1.12!12.24!Hoxb9;;chr3:95032184..95032195,-!p4@Mllt11!1.11!14.66!Mllt11;;chrX:108009761..108009788,+!p1@Pou3f4!1.11!11.96!Pou3f4;;chr6:52195795..52195825,-!p1@Hoxa11!1.10!11.53!Hoxa11;;chr15:102767273..102767285,+!p2@Hoxc12!1.09!11.39!Hoxc12;;chr15:75578748..75578752,-!p1@Mafa!1.09!11.25!Mafa;;chr15:102751603..102751630,+!p1@Hoxc13!1.07!10.82!Hoxc13;;chr11:33103563..33103583,-!p1@Tlx3!1.07!10.68!Tlx3;;chr6:52163319..52163342,-!p1@Hoxa3!1.06!15.38!Hoxa3;;chr2:24331085..24331100,-!p1@Pax8!1.06!10.54!Pax8;;chr7:144506077..144506128,-!p1@Ebf3!1.05!23.63!Ebf3;;chr6:52167459..52167492,-!p1@Hoxa7!1.05!12.24!Hoxa7;;chr10:84218800..84218829,+!p2@Rfx4!1.05!10.25!Rfx4;;chr15:76352832..76352900,-!p1@Scrt1!1.03!9.68!Scrt1;;chr13:48356475..48356492,+!p1@Id4!1.02!207.44!Id4;;chr13:44936126..44936164,+!p6@Jarid2!1.02!10.96!Jarid2;;chr15:76352740..76352781,-!p5@Scrt1!1.02!9.54!Scrt1;;chr14:122874619..122874634,+!p1@Zic2!1.02!9.54!Zic2;;chr15:102828658..102828678,+!p1@Hoxc6!1.02!9.40!Hoxc6;;chr2:162769220..162769252,+!p1@L3mbtl1!1.02!9.40!L3mbtl1;;chr18:81183755..81183761,-!p1@Sall3!1.02!9.40!Sall3;;chr2:127347067..127347093,-!p1@Kcnip3!1.01!15.52!Kcnip3;;chr11:96145450..96145517,+!p2@Hoxb7!1.00!13.81!Hoxb7;;chr15:76353005..76353021,-!p2@Scrt1!1.00!8.97!Scrt1;;chr7:91558472..91558512,-!p2@Arnt2!0.99!12.67!Arnt2;;chr2:81893535..81893548,+!p1@Zfp804a!0.99!8.83!Zfp804a;;chr11:116196664..116196679,-!p1@Foxj1!0.97!13.10!Foxj1;;chr12:72149325..72149343,+!p2@Arid4a!0.97!11.67!Arid4a;;chr2:79296783..79296801,-!p1@Neurod1!0.97!8.40!Neurod1;;chr6:52195763..52195792,-!p2@Hoxa11!0.97!8.40!Hoxa11;;chr11:44431115..44431132,+!p9@Ebf1!0.97!8.40!Ebf1;;chr4:150482353..150482386,-!p6@Camta1!0.97!8.26!Camta1;;chrX:34442842..34442866,-!p3@Nkrf!0.95!7.97!Nkrf;;chr11:96132637..96132652,+!p1@Hoxb9!0.95!7.83!Hoxb9;;chr4:99322820..99322845,+!p1@Foxd3!0.94!9.97!Foxd3;;chr4:58956447..58956510,+!p1@Zkscan16!0.93!16.66!Zkscan16;;chr3:101814061..101814094,+!p1@Nhlh2!0.93!7.55!Nhlh2;;chrX:58146612..58146615,-!p1@Sox3!0.93!7.55!Sox3;;chr4:13670499..13670526,+!p2@Runx1t1!0.92!16.66!Runx1t1;;chr5:120881900..120881914,+!p1@Lhx5!0.92!7.40!Lhx5;;chr12:28027561..28027591,-!p1@Sox11!0.91!48.98!Sox11;;chr4:22415443..22415506,-!p1@Pou3f2!0.91!7.12!Pou3f2;;chr7:91558392..91558434,-!p1@Arnt2!0.90!20.07!Arnt2;;chr12:87762578..87762612,+!p1@Esrrb!0.90!6.98!Esrrb;;chr4:13670571..13670625,+!p1@Runx1t1!0.89!19.08!Runx1t1;;chr3:95032213..95032226,-!p6@Mllt11!0.89!8.26!Mllt11;;chr15:102751578..102751600,+!p2@Hoxc13!0.89!6.83!Hoxc13;;chr9:91263879..91263911,+!p1@Zic4!0.89!6.83!Zic4;;chr13:95645580..95645598,+!p1@Otp!0.89!6.69!Otp;;chr12:3806003..3806031,+!p11@Dnmt3a!0.88!6.55!Dnmt3a;;chr5:24032551..24032557,-!p@chr5:24032551..24032557,-!0.88!6.55!Gbx1;;chrX:55283799..55283813,+!p1@Zic3!0.88!6.55!Zic3;;chr2:74542918..74542971,+!p1@Hoxd8!0.87!9.82!Hoxd8;;chr9:20385868..20385902,+!p3@Zfp846!0.87!9.54!Zfp846;;chr5:138199481..138199491,+!p16@Tsc22d4!0.87!6.41!Tsc22d4;;chr2:74520343..74520383,+!p4@Hoxd11!0.87!6.41!Hoxd11;;chr6:53018556..53018650,-!p1@Jazf1!0.86!44.85!Jazf1;;chr7:130644017..130644092,-!p1@Zkscan2!0.86!12.53!Zkscan2;;chr6:52167513..52167549,-!p2@Hoxa7!0.86!9.11!Hoxa7;;chr2:147012125..147012149,-!p1@Nkx2-2!0.86!6.26!Nkx2-2;;chr6:53018700..53018759,-!p2@Jazf1!0.85!23.21!Jazf1;;chr6:52176144..52176161,-!p2@Hoxa9!0.85!6.12!Hoxa9;;chr6:52167434..52167450,-!p3@Hoxa7!0.85!6.12!Hoxa7;;chr4:13678723..13678739,+!p10@Runx1t1!0.85!6.12!Runx1t1;;chr5:77524250..77524300,-!p1@Hopx!0.84!127.85!Hopx;;chr7:37483231..37483263,+!p2@Tshz3!0.84!9.25!Tshz3;;chr15:102820964..102821006,+!p1@Hoxc8!0.84!5.98!Hoxc8;;chr4:124334894..124334899,+!p1@Pou3f1!0.83!7.69!Pou3f1;;chr9:99776566..99776612,-!p1@Sox14!0.83!5.84!Sox14;;chr11:96160403..96160416,+!p4@Hoxb6!0.83!5.84!Hoxb6;;chr14:34791937..34791977,-!p1@Zfp488!0.83!5.84!Zfp488;;chr14:118636238..118636257,-!p2@Sox21!0.83!5.69!Sox21;;chr2:181501745..181501778,+!p1@Myt1!0.83!5.69!Myt1;;chr2:147019977..147019985,-!p2@Nkx2-2!0.83!5.69!Nkx2-2;;chr17:37140628..37140631,+!p2@Zfp57!0.82!11.82!Zfp57;;chr7:30092993..30093076,+!p1@Dpf1!0.82!10.11!Dpf1;;chr13:78339428..78339466,-!p2@Nr2f1!0.82!7.97!Nr2f1;;chr11:44430877..44430899,+!p6@Ebf1!0.82!7.40!Ebf1;;chr4:129118044..129118067,-!p1@Zbtb8b!0.82!7.26!Zbtb8b;;chr7:122968213..122968266,-!p4@Sox6!0.82!6.69!Sox6;;chr5:77543897..77543911,-!p2@Hopx!0.81!10.82!Hopx;;chr14:67853632..67853674,+!p3@Ebf2!0.81!6.69!Ebf2;;chr2:74517609..74517621,+!p3@Hoxd11!0.81!5.41!Hoxd11;;chr2:168427068..168427115,-!p3@Nfatc2!0.81!5.41!Nfatc2;;chr1:173987720..173987729,-!p1@Nhlh1!0.80!5.27!Nhlh1;;chr11:96145393..96145407,+!p3@Hoxb7!0.80!5.27!Hoxb7;;chr11:96160119..96160135,+!p7@Hoxb6!0.80!5.27!Hoxb6;;chr11:96145362..96145389,+!p4@Hoxb7!0.79!5.13!Hoxb7;;chr3:95032558..95032641,-!p2@Mllt11!0.78!30.33!Mllt11;;chr17:37139519..37139531,+!p5@Zfp57!0.78!6.12!Zfp57;;chr2:74520048..74520064,+!p1@Hoxd11!0.78!4.98!Hoxd11;;chr11:101646566..101646603,-!p1@Etv4!0.77!16.94!Etv4;;chr7:25372631..25372684,-!p1@Zfp575!0.77!15.95!Zfp575;;chr10:62327990..62328025,-!p2@Tet1!0.77!7.97!Tet1;;chr17:32525943..32525992,-!p4@Wiz!0.77!7.69!Wiz;;chr7:148513409..148513455,-!p2@Deaf1!0.76!24.20!Deaf1;;chr6:52161666..52161711,-!p1@Hoxa6!0.76!4.70!Hoxa6;;chr5:24104751..24104773,-!p5@Smarcd3!0.76!4.70!Smarcd3;;chr1:19199119..19199134,+!p4@Tfap2b!0.76!4.70!Tfap2b;;chrX:109714331..109714347,+!p1@Zfp711!0.75!20.93!Zfp711;;chr10:30562571..30562597,-!p1@Hey2!0.75!11.82!Hey2;;chr11:23978111..23978134,+!p3@Bcl11a!0.75!10.25!Bcl11a;;chrX:55284180..55284195,+!p2@Zic3!0.74!4.56!Zic3;;chr9:55785981..55786009,-!p2@Scaper!0.73!12.67!Scaper;;chr7:25292160..25292213,+!p3@Zfp428!0.73!11.67!Zfp428;;chr10:67375368..67375433,-!p1@Zfp365!0.73!8.12!Zfp365;;chr10:86956396..86956411,-!p1@Ascl1!0.73!7.12!Ascl1;;chr7:30089006..30089022,+!p3@Dpf1!0.73!4.41!Dpf1;;chr8:12395603..12395621,+!p1@Sox1!0.73!4.41!Sox1;;chr7:144506051..144506062,-!p5@Ebf3!0.73!4.41!Ebf3;;chr15:102797170..102797182,+!p3@Hoxc10!0.73!4.41!Hoxc10;;chr15:102797183..102797205,+!p4@Hoxc10!0.73!4.41!Hoxc10;;chr2:74536026..74536039,+!p1@Hoxd9!0.73!4.41!Hoxd9;;chr4:82145196..82145229,-!p7@Nfib!0.73!4.41!Nfib;;chr11:98603160..98603171,+!p3@Thra!0.72!21.93!Thra;;chr4:54960870..54960926,+!p1@Zfp462!0.72!16.80!Zfp462;;chr9:106355684..106355744,+!p5@Pcbp4!0.72!6.83!Pcbp4;;chr11:23978229..23978268,+!p8@Bcl11a!0.72!4.98!Bcl11a;;chr4:150503457..150503498,-!p3@Camta1!0.72!4.84!Camta1;;chr7:108966820..108966835,+!p1@Phox2a!0.72!4.27!Phox2a;;chr7:144505876..144505884,-!p9@Ebf3!0.72!4.27!Ebf3;;chr2:127347042..127347058,-!p3@Kcnip3!0.72!4.27!Kcnip3;;chr4:150513630..150513686,-!p4@Camta1!0.71!4.84!Camta1;;chr2:74517725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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000207
 |is_obsolete=
-|library_ids=CNhs12638
+|library_id=CNhs12638
+|library_id_phase_based=2:CNhs12638
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11743
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11743
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520ventral%2520spinal%2520cord%252c%2520donor2.CNhs12638.11743-123F6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520ventral%2520spinal%2520cord%252c%2520donor2.CNhs12638.11743-123F6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520ventral%2520spinal%2520cord%252c%2520donor2.CNhs12638.11743-123F6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520ventral%2520spinal%2520cord%252c%2520donor2.CNhs12638.11743-123F6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520ventral%2520spinal%2520cord%252c%2520donor2.CNhs12638.11743-123F6.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - ventral spinal cord, donor2
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12638,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0473071002565921,0,0,0,0,0,0.023601231567899,0,0,0,0,0.0244771419219718,0,0,0,0,0,0,0.108398099941022,0,0,0,0,0,0,0,0,0,0,0,0,0.266879645037218,-0.403963808512464,0,0,0,0,0.0652515532321165,-0.0776850424307855,0.280984635400096,0.147353231913837,0.890217696805099,0.647161656312358,0.300291450823596,0,0,0,0,0,0,0,0,0,0,0,-0.00819811908470574,0,0,0,0,-0.0328883182767021,0,0,0,0,0.00756434030978495,0.141974966093017,-0.310650657339386,0.472799222369514,-0.0232909257623186,0,0.0578074284787346,0.135462727059154,0.116012387868085,0,0,0.10129756114415,0.216060447258115,0.191218191516453,-0.0210241663611728,0.0153594896706015,0,0,0,0,0,0.0971336497854758,-0.103764827512503,-0.0584916987232167,0,0,0.23346783925084,0.27965413744919,0
@@ Line 85: / Line 97: @@
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 |xref=
-}} {{DRAAccessionNumbers
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11743-123F6;search_select_hide=table117:11743-123F6
-|DRA_sample_Accession=CAGE@DRS008740
-|accession_numbers=DRX008850;DRR009722;DRZ001147;DRZ002532;CAGE
-|library_id=CNhs12638
 }}

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FF:11743-123F6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:17, 4 June 2020

CNhs12638

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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