FF:11489-119E4: Difference between revisions

Latest revision as of 18:04, 4 June 2020

Name:	Mouse Neurons - substantia nigra, donor4
Species:	Mouse (Mus musculus)
Library ID:	CNhs12612,CNhs12821
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	substantia nigra
dev stage	NA
sex	NA
age	NA
cell type	NA
cell line	NA
company	Sciencell/3H
collaboration	NA
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	RNASUB3
catalog number	custom
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005603

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12612		CAGE		DRX008846		DRR009718
CNhs12821		CAGE		DRX023598		DRR025993

Accession ID Mm9

Library id		BAM		CTSS
CNhs12612		DRZ001143		DRZ002528
CNhs12821		DRZ005245		DRZ006035

Accession ID Mm10

Library id		BAM		CTSS
CNhs12612		DRZ012493		DRZ013878
CNhs12821		DRZ009986		DRZ010650

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

CNhs12612

0	0
1	0.695
10	0
100	0
1000	0
1001	0.0169
1002	-0.0474
1003	0.0735
1004	0
1005	0.0412
1006	0.66
1007	-0.19
1008	0
1009	-0.067
101	-0.216
1010	0
1011	0.281
1012	0
1013	0.111
1014	0
1015	-0.0301
1016	0.00142
1017	0
1018	0
1019	0
102	0
1020	0.546
1021	0.12
1022	0.148
1023	0
1024	0
1025	0
1026	0
1027	0.42
1028	0
1029	-0.148
103	-0.0736
1030	0
1031	-0.378
1032	0.531
1033	0.0626
1034	0
1035	0
1036	-0.0759
1037	0
1038	-0.0327
1039	0.18
104	0
1040	-0.369
1041	0

CNhs12821

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: CNhs12612

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0127
MA0003.1	MA0003.1	0.488
MA0004.1	MA0004.1	0.445
MA0006.1	MA0006.1	0.193
MA0007.1	MA0007.1	0.312
MA0009.1	MA0009.1	0.933
MA0014.1	MA0014.1	0.824
MA0017.1	MA0017.1	3.12378e-6
MA0018.2	MA0018.2	0.00288
MA0019.1	MA0019.1	0.793
MA0024.1	MA0024.1	0.0233
MA0025.1	MA0025.1	5.68038e-4
MA0027.1	MA0027.1	0.0694
MA0028.1	MA0028.1	0.129
MA0029.1	MA0029.1	0.851
MA0030.1	MA0030.1	0.872
MA0031.1	MA0031.1	0.342
MA0035.2	MA0035.2	0.0721
MA0038.1	MA0038.1	0.916
MA0039.2	MA0039.2	0.0514
MA0040.1	MA0040.1	0.627
MA0041.1	MA0041.1	0.144
MA0042.1	MA0042.1	0.309
MA0043.1	MA0043.1	0.034
MA0046.1	MA0046.1	3.72067e-6
MA0047.2	MA0047.2	9.84777e-4
MA0048.1	MA0048.1	0.0262
MA0050.1	MA0050.1	3.33456e-6
MA0051.1	MA0051.1	1.16883e-4
MA0052.1	MA0052.1	0.98
MA0055.1	MA0055.1	0.0187
MA0057.1	MA0057.1	0.396
MA0058.1	MA0058.1	0.51
MA0059.1	MA0059.1	0.206
MA0060.1	MA0060.1	0.797
MA0061.1	MA0061.1	0.0143
MA0062.2	MA0062.2	0.00355
MA0065.2	MA0065.2	2.71854e-5
MA0066.1	MA0066.1	0.1
MA0067.1	MA0067.1	0.243
MA0068.1	MA0068.1	0.983
MA0069.1	MA0069.1	0.13
MA0070.1	MA0070.1	0.21
MA0071.1	MA0071.1	0.402
MA0072.1	MA0072.1	0.933
MA0073.1	MA0073.1	0.865
MA0074.1	MA0074.1	0.242
MA0076.1	MA0076.1	0.365
MA0077.1	MA0077.1	0.13
MA0078.1	MA0078.1	0.94
MA0079.2	MA0079.2	0.162
MA0080.2	MA0080.2	6.18274e-10
MA0081.1	MA0081.1	0.169
MA0083.1	MA0083.1	0.00205
MA0084.1	MA0084.1	0.423
MA0087.1	MA0087.1	0.18
MA0088.1	MA0088.1	0.368
MA0090.1	MA0090.1	0.0511
MA0091.1	MA0091.1	0.226
MA0092.1	MA0092.1	0.206
MA0093.1	MA0093.1	0.499
MA0099.2	MA0099.2	0.0238
MA0100.1	MA0100.1	0.0826
MA0101.1	MA0101.1	0.00917
MA0102.2	MA0102.2	0.458
MA0103.1	MA0103.1	0.397
MA0104.2	MA0104.2	0.925
MA0105.1	MA0105.1	0.00246
MA0106.1	MA0106.1	0.0531
MA0107.1	MA0107.1	0.0143
MA0108.2	MA0108.2	0.00713
MA0111.1	MA0111.1	0.971
MA0112.2	MA0112.2	0.00161
MA0113.1	MA0113.1	0.389
MA0114.1	MA0114.1	4.03739e-6
MA0115.1	MA0115.1	7.14526e-4
MA0116.1	MA0116.1	0.101
MA0117.1	MA0117.1	0.854
MA0119.1	MA0119.1	0.183
MA0122.1	MA0122.1	0.785
MA0124.1	MA0124.1	0.633
MA0125.1	MA0125.1	0.033
MA0131.1	MA0131.1	0.512
MA0135.1	MA0135.1	0.0723
MA0136.1	MA0136.1	2.59924e-11
MA0137.2	MA0137.2	0.0779
MA0138.2	MA0138.2	5.07395e-5
MA0139.1	MA0139.1	0.77
MA0140.1	MA0140.1	7.6329e-5
MA0141.1	MA0141.1	0.239
MA0142.1	MA0142.1	0.556
MA0143.1	MA0143.1	0.854
MA0144.1	MA0144.1	0.0351
MA0145.1	MA0145.1	0.17
MA0146.1	MA0146.1	0.0913
MA0147.1	MA0147.1	0.805
MA0148.1	MA0148.1	0.00148
MA0149.1	MA0149.1	0.408
MA0150.1	MA0150.1	0.272
MA0152.1	MA0152.1	0.0313
MA0153.1	MA0153.1	1.78499e-7
MA0154.1	MA0154.1	0.0484
MA0155.1	MA0155.1	0.602
MA0156.1	MA0156.1	4.04048e-9
MA0157.1	MA0157.1	0.229
MA0159.1	MA0159.1	0.0297
MA0160.1	MA0160.1	0.135
MA0162.1	MA0162.1	0.279
MA0163.1	MA0163.1	0.00229
MA0164.1	MA0164.1	0.854
MA0258.1	MA0258.1	0.0499
MA0259.1	MA0259.1	0.786

library id: CNhs12821This sample isn't target for the analysis

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: CNhs12612

Novel motif	Logo	P-value
1	1	0.273
10	10	0.0355
100	100	0.316
101	101	0.986
102	102	0.791
103	103	0.088
104	104	0.85
105	105	0.462
106	106	0.0316
107	107	0.0762
108	108	0.312
109	109	0.0332
11	11	0.23
110	110	0.0424
111	111	0.478
112	112	0.0121
113	113	0.6
114	114	0.836
115	115	0.88
116	116	0.638
117	117	0.00296
118	118	0.355
119	119	0.186
12	12	0.94
120	120	0.808
121	121	0.472
122	122	0.742
123	123	4.28563e-4
124	124	0.0815
125	125	0.188
126	126	0.065
127	127	0.503
128	128	0.016
129	129	0.231
13	13	3.41613e-8
130	130	0.0973
131	131	0.528
132	132	0.594
133	133	0.764
134	134	0.21
135	135	0.237
136	136	0.716
137	137	0.564
138	138	0.566
139	139	0.347
14	14	0.756
140	140	0.136
141	141	0.764
142	142	0.32
143	143	0.447
144	144	0.642
145	145	7.47928e-5
146	146	0.433
147	147	0.241
148	148	0.761
149	149	0.718
15	15	0.175
150	150	0.0629
151	151	0.971
152	152	0.164
153	153	0.417
154	154	0.54
155	155	0.721
156	156	0.0164
157	157	0.241
158	158	0.0887
159	159	0.178
160	160	0.216
161	161	0.652
162	162	0.739
163	163	0.762
164	164	0.0249
165	165	0.319
166	166	0.29
167	167	0.95
168	168	0.554
169	169	0.00247
17	17	0.103
18	18	0.588
19	19	0.106
2	2	0.45
20	20	0.0156
21	21	0.322
22	22	0.211
23	23	0.651
24	24	0.112
25	25	0.875
26	26	2.269e-10
27	27	0.192
28	28	0.864
29	29	0.0493
3	3	0.107
30	30	0.708
31	31	0.541
32	32	0.814
33	33	0.136
34	34	0.968
35	35	0.693
36	36	0.163
37	37	0.0588
38	38	0.483
39	39	0.37
4	4	0.366
40	40	0.16
41	41	0.639
42	42	0.208
43	43	0.104
44	44	0.825
45	45	0.775
46	46	0.0248
47	47	0.615
48	48	0.433
49	49	0.137
5	5	0.166
50	50	0.298
51	51	0.651
52	52	0.299
53	53	0.488
54	54	0.951
55	55	0.97
56	56	0.659
57	57	0.539
58	58	0.309
59	59	0.289
6	6	0.748
60	60	0.0359
61	61	0.0607
62	62	0.23
63	63	0.22
64	64	0.995
65	65	0.578
66	66	0.942
67	67	0.979
68	68	0.974
69	69	0.809
7	7	0.00931
70	70	0.269
71	71	0.00139
72	72	0.667
73	73	0.0919
74	74	0.732
75	75	0.0618
76	76	0.286
77	77	0.775
78	78	0.00322
79	79	0.112
8	8	0.0838
80	80	0.943
81	81	0.737
82	82	0.414
83	83	0.359
84	84	0.642
85	85	0.251
86	86	0.105
87	87	0.47
88	88	0.718
89	89	0.778
9	9	0.355
90	90	0.144
91	91	0.0842
92	92	0.468
93	93	0.0597
94	94	0.449
95	95	0.139
96	96	0.415
97	97	0.979
98	98	0.725
99	99	0.527

library id: CNhs12821This sample isn't target for the analysis

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: CNhs12612
library id: CNhs12821

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000208 mouse neuron of the substantia nigra 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)
0002614 (neuron of the substantia nigra)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0002038 (substantia nigra)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009663 (telencephalic nucleus)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0009661 (midbrain nucleus)
0000125 (neural nucleus)
0002950 (regional part of midbrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0002308 (nucleus of brain)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001893 (telencephalon)
0001890 (forebrain)
0001891 (midbrain)
0010011 (collection of basal ganglia)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000208 (mouse neuron of the substantia nigra 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@DRS008736
+|DRA_sample_Accession=CAGE@SAMD00005603
+|accession_numbers=CAGE;DRX008846;DRR009718;DRZ001143;DRZ002528;DRZ012493;DRZ013878!CAGE;DRX023598;DRR025993;DRZ005245;DRZ006035;DRZ009986;DRZ010650
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0002038,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009663,UBERON:0002420,UBERON:0002616,UBERON:0002780,UBERON:0009661,UBERON:0000125,UBERON:0002950,UBERON:0002020,UBERON:0007245,UBERON:0010317,UBERON:0002308,UBERON:0010009,UBERON:0001017,UBERON:0001016,UBERON:0001893,UBERON:0001890,UBERON:0001891,UBERON:0010011,UBERON:0000454
 |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:0002614
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.51!365.17!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!1.98!171.42!Tsc22d4;;chr2:79296783..79296801,-!p1@Neurod1!1.61!39.64!Neurod1;;chr16:91225808..91225824,+!p1@Olig2!1.59!37.97!Olig2;;chr15:76353005..76353021,-!p2@Scrt1!1.58!37.41!Scrt1;;chr9:91260616..91260653,-!p2@Zic1!1.57!36.01!Zic1;;chr15:76352434..76352488,-!p4@Scrt1!1.53!32.66!Scrt1;;chr17:48015839..48015915,-!p3@Foxp4!1.52!37.97!Foxp4;;chr9:91260594..91260612,-!p1@Zic1!1.51!30.99!Zic1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.50!38.81!Pou3f3;;chr7:146768691..146768707,-!p1@Nkx6-2!1.48!29.31!Nkx6-2;;chr3:95032091..95032183,-!p1@Mllt11!1.44!220.28!Mllt11;;chr7:116154364..116154444,+!p1@Tub!1.44!45.23!Tub;;chrX:34442872..34442899,-!p1@Nkrf!1.41!31.55!Nkrf;;chr17:25707623..25707639,-!p1@Sox8!1.40!99.67!Sox8;;chr16:91270091..91270143,+!p2@Olig1!1.31!19.26!Olig1;;chr15:76352677..76352737,-!p3@Scrt1!1.29!18.71!Scrt1;;chr2:168427068..168427115,-!p3@Nfatc2!1.27!17.59!Nfatc2;;chr4:150482563..150482655,-!p2@Camta1!1.26!59.75!Camta1;;chr2:163051181..163051205,+!p2@Tox2!1.24!16.47!Tox2;;chr15:78994907..78994926,-!p1@Sox10!1.23!40.48!Sox10;;chr8:107793688..107793736,+!p1@Hsf4!1.23!20.94!Hsf4;;chr13:72766250..72766273,+!p1@Irx2!1.22!24.29!Irx2;;chr18:36441119..36441158,+!p2@Pura!1.21!37.13!Pura;;chr10:67375368..67375433,-!p1@Zfp365!1.21!26.52!Zfp365;;chr11:96685444..96685473,-!p5@Nfe2l1!1.21!15.36!Nfe2l1;;chr5:28492230..28492257,+!p1@En2!1.21!15.36!En2;;chr10:67375146..67375208,-!p2@Zfp365!1.19!22.06!Zfp365;;chr8:24780125..24780143,+!p1@Zmat4!1.17!20.10!Zmat4;;chr3:95032515..95032553,-!p5@Mllt11!1.17!16.75!Mllt11;;chrX:108009761..108009788,+!p1@Pou3f4!1.17!13.96!Pou3f4;;chr11:98190918..98190951,-!p1@Neurod2!1.17!13.68!Neurod2;;chr3:95032197..95032208,-!p3@Mllt11!1.14!15.91!Mllt11;;chr3:95032213..95032226,-!p6@Mllt11!1.13!15.08!Mllt11;;chrX:137083127..137083138,-!p9@Tsc22d3!1.13!12.56!Tsc22d3;;chr4:150513630..150513686,-!p4@Camta1!1.12!13.96!Camta1;;chr9:106362954..106362977,+!p6@Pcbp4!1.12!12.28!Pcbp4;;chr14:122874619..122874634,+!p1@Zic2!1.12!12.28!Zic2;;chr2:163030219..163030258,+!p5@Tox2!1.11!12.00!Tox2;;chr12:54349410..54349461,+!p1@Npas3!1.10!13.96!Npas3;;chr3:95032558..95032641,-!p2@Mllt11!1.09!63.37!Mllt11;;chr15:103170533..103170556,-!p1@Zfp385a!1.09!42.71!Zfp385a;;chr7:17062114..17062141,-!p1@Npas1!1.09!11.17!Npas1;;chr1:122498955..122498968,+!p1@En1!1.09!11.17!En1;;chr1:179374784..179374800,+!p2@Zfp238!1.08!13.12!Zfp238;;chr2:127347067..127347093,-!p1@Kcnip3!1.07!18.15!Kcnip3;;chr19:19185671..19185693,-!p1@Rorb!1.06!25.41!Rorb;;chr2:65683890..65683907,+!p1@Csrnp3!1.05!19.54!Csrnp3;;chr3:34548909..34548927,+!p1@Sox2!1.04!17.03!Sox2;;chr7:148008023..148008092,-!p1@Zfp941!1.02!23.17!Zfp941;;chr6:134780163..134780197,+!p2@Crebl2!1.02!22.61!Crebl2;;chr3:95032184..95032195,-!p4@Mllt11!1.02!11.73!Mllt11;;chrX:34442842..34442866,-!p3@Nkrf!1.02!9.49!Nkrf;;chr2:25562263..25562314,+!p2@Bmyc!1.00!36.01!Bmyc;;chr14:122874593..122874610,+!p2@Zic2!1.00!8.93!Zic2;;chr10:84218800..84218829,+!p2@Rfx4!1.00!8.93!Rfx4;;chr4:154335024..154335039,+!p1@Hes5!0.98!10.33!Hes5;;chr16:91225654..91225671,+!p2@Olig2!0.98!8.65!Olig2;;chr6:145814003..145814056,-!p1@Bhlhe41!0.97!24.85!Bhlhe41;;chr12:30219426..30219506,+!p2@Myt1l!0.97!8.38!Myt1l;;chr6:145813905..145813932,-!p2@Bhlhe41!0.96!15.63!Bhlhe41;;chr3:54559463..54559493,+!p3@Smad9!0.96!15.08!Smad9;;chr5:122499831..122499891,-!p1@Cux2!0.96!12.56!Cux2;;chr2:151907546..151907561,+!p1@Scrt2!0.96!8.10!Scrt2;;chr4:58956447..58956510,+!p1@Zkscan16!0.93!17.03!Zkscan16;;chr1:189821714..189821761,+!p1@Esrrg!0.93!14.24!Esrrg;;chr3:101814061..101814094,+!p1@Nhlh2!0.93!7.54!Nhlh2;;chr5:140019843..140019858,+!p2@Uncx!0.93!7.54!Uncx;;chr11:96685487..96685512,-!p7@Nfe2l1!0.93!7.54!Nfe2l1;;chr11:98636531..98636559,-!p1@Nr1d1!0.92!43.55!Nr1d1;;chr15:103170516..103170531,-!p2@Zfp385a!0.92!18.15!Zfp385a;;chr8:112603658..112603674,+!p2@Zfp612!0.91!13.40!Zfp612;;chr19:10315179..10315241,-!p1@Gm98!0.90!76.50!Gm98;;chr7:91558472..91558512,-!p2@Arnt2!0.90!10.05!Arnt2;;chr2:163030186..163030204,+!p4@Tox2!0.90!6.98!Tox2;;chr2:163030164..163030178,+!p6@Tox2!0.90!6.98!Tox2;;chr13:72766279..72766296,+!p2@Irx2!0.89!10.33!Irx2;;chr3:34548946..34548972,+!p2@Sox2!0.89!7.54!Sox2;;chr2:127347042..127347058,-!p3@Kcnip3!0.89!6.70!Kcnip3;;chr10:80893711..80893784,-!p3@Nfic!0.87!34.90!Nfic;;chr13:72101178..72101203,-!p1@Irx1!0.87!10.33!Irx1;;chr2:127347094..127347111,-!p2@Kcnip3!0.86!10.61!Kcnip3;;chr7:38558544..38558566,-!p4@Zfp536!0.86!7.26!Zfp536;;chr7:52960555..52960662,+!p1@Dbp!0.85!55.28!Dbp;;chr7:38554763..38554780,-!p1@Zfp536!0.85!11.45!Zfp536;;chr4:150482353..150482386,-!p6@Camta1!0.85!6.14!Camta1;;chr11:84339016..84339044,-!p1@Lhx1!0.85!6.14!Lhx1;;chr10:84218895..84218909,+!p1@Rfx4!0.85!6.14!Rfx4;;chr10:67375223..67375240,-!p4@Zfp365!0.84!6.70!Zfp365;;chr4:44717334..44717367,-!p5@Pax5!0.84!5.86!Pax5;;chr1:6477388..6477419,+!p3@St18!0.84!5.86!St18;;chr7:52960700..52960719,+!p2@Dbp!0.83!7.26!Dbp;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.82!62.54!Camta2;;chr11:90251852..90251855,-!p4@Hlf!0.82!6.98!Hlf;;chr8:12395603..12395621,+!p1@Sox1!0.82!5.58!Sox1;;chr7:52960888..52960902,+!p7@Dbp!0.82!5.58!Dbp;;chr2:65768174..65768247,+!p2@Csrnp3!0.82!5.58!Csrnp3;;chr2:168427120..168427138,-!p4@Nfatc2!0.82!5.58!Nfatc2;;chr4:22415443..22415506,-!p1@Pou3f2!0.82!5.58!Pou3f2;;chr15:82742573..82742620,-!p2@Tcf20!0.82!5.58!Tcf20;;chr7:91558392..91558434,-!p1@Arnt2!0.81!15.91!Arnt2;;chr7:38558574..38558611,-!p2@Zfp536!0.81!6.98!Zfp536;;chr6:145813964..145813994,-!p3@Bhlhe41!0.80!6.98!Bhlhe41;;chr10:67375342..67375365,-!p3@Zfp365!0.80!5.30!Zfp365;;chr2:25562315..25562344,+!p3@Bmyc!0.79!18.43!Bmyc;;chr8:87297878..87297935,-!p3@Nfix!0.78!11.73!Nfix;;chr9:106356278..106356292,+!p3@Pcbp4!0.78!8.93!Pcbp4;;chr2:77654815..77654872,-!p2@Zfp385b!0.78!6.42!Zfp385b;;chr13:95645580..95645598,+!p1@Otp!0.78!5.03!Otp;;chr19:26681865..26681900,+!p6@Smarca2!0.77!15.36!Smarca2;;chr11:98603119..98603130,+!p2@Thra!0.76!44.11!Thra;;chrX:137077151..137077227,-!p2@Tsc22d3!0.76!36.85!Tsc22d3;;chr14:34791937..34791977,-!p1@Zfp488!0.76!4.75!Zfp488;;chr2:162769220..162769252,+!p1@L3mbtl1!0.76!4.75!L3mbtl1;;chr8:94325321..94325366,-!p1@Irx3!0.75!12.00!Irx3;;chr15:103164702..103164778,-!p3@Zfp385a!0.75!5.58!Zfp385a;;chr11:98603160..98603171,+!p3@Thra!0.74!23.45!Thra;;chr17:27693525..27693538,+!p5@Hmga1!0.74!16.75!Hmga1;;chr5:120881900..120881914,+!p1@Lhx5!0.74!4.47!Lhx5;;chr2:81893535..81893548,+!p1@Zfp804a!0.74!4.47!Zfp804a;;chr9:106355684..106355744,+!p5@Pcbp4!0.73!6.98!Pcbp4;;chr8:125897750..125897758,+!p2@Tcf25!0.72!31.83!Tcf25;;chr14:76903992..76904056,+!p6@Tsc22d1!0.72!9.49!Tsc22d1;;chr19:5424822..5424845,-!p3@Drap1!0.71!18.15!Drap1;;chr13:72101141..72101158,-!p3@Irx1!0.71!5.30!Irx1;;chr8:107793737..107793757,+!p2@Hsf4!0.71!4.75!Hsf4;;chr7:91520922..91520956,-!p5@Arnt2!0.71!4.19!Arnt2;;chr8:12395892..12395919,+!p4@Sox1!0.71!4.19!Sox1;;chr2:181501745..181501778,+!p1@Myt1!0.71!4.19!Myt1;;chrX:70656436..70656464,+!p1@Zfp92!0.71!4.19!Zfp92;;chr5:98609885..98609900,+!p1@Prdm8!0.71!4.19!Prdm8;;chr7:17200307..17200370,-!p2@Grlf1!0.70!33.50!Grlf1;;chr1:170361991..170362015,-!p6@Pbx1!0.70!9.77!Pbx1;;chr12:72149325..72149343,+!p2@Arid4a!0.70!5.86!Arid4a;;chr11:90252223..90252240,-!p1@Hlf!0.69!36.85!Hlf;;chr11:69579401..69579427,+!p2@Zbtb4!0.69!16.75!Zbtb4;;chr11:116196664..116196679,-!p1@Foxj1!0.69!6.42!Foxj1;;chr5:107003725..107003746,-!p5@Zfp644!0.69!5.30!Zfp644;;chr8:94325273..94325288,-!p5@Irx3!0.69!5.03!Irx3;;chr11:98636508..98636524,-!p3@Nr1d1!0.69!5.03!Nr1d1;;chr3:34549096..34549111,+!p3@Sox2!0.69!3.91!Sox2;;chr14:118636238..118636257,-!p2@Sox21!0.69!3.91!Sox21;;chrX:95345005..95345053,+!p1@Ar!0.69!3.91!Ar;;chr6:117813087..117813121,+!p1@Zfp239!0.68!16.19!Zfp239;;chr3:54559496..54559511,+!p1@Smad9!0.68!9.21!Smad9;;chr5:3648045..3648074,-!p2@Gatad1!0.68!6.70!Gatad1;;chr19:5423800..5423821,-!p5@Drap1!0.68!5.86!Drap1;;chr14:52935860..52935874,-!p3@Sall2!0.68!5.86!Sall2;;chr14:52935876..52935928,-!p1@Sall2!0.67!34.34!Sall2;;chr15:103170561..103170572,-!p4@Zfp385a!0.67!5.58!Zfp385a;;chr2:115890294..115890334,-!p9@Meis2!0.67!5.30!Meis2;;chr7:108966820..108966835,+!p1@Phox2a!0.67!3.63!Phox2a;;chr6:55631042..55631102,-!p1@Neurod6!0.67!3.63!Neurod6;;chr4:107353376..107353452,-!p3@Dmrtb1!0.67!3.63!Dmrtb1;;chr11:21901608..21901634,-!p1@Otx1!0.67!3.63!Otx1;;chr12:86939997..86940040,+!p4@Jdp2!0.67!3.63!Jdp2;;chr8:12395874..12395885,+!p2@Sox1!0.67!3.63!Sox1;;chr11:69579472..69579529,+!p1@Zbtb4!0.66!20.66!Zbtb4;;chr13:72101161..72101177,-!p2@Irx1!0.65!5.03!Irx1;;chr4:124334894..124334899,+!p1@Pou3f1!0.65!4.75!Pou3f1;;chr5:77524250..77524300,-!p1@Hopx!0.64!80.13!Hopx;;chr14:19071466..19071550,-!p1@Nr1d2!0.64!27.08!Nr1d2;;chr7:52963269..52963305,+!p4@Dbp!0.64!5.03!Dbp;;chr2:9809357..9809371,-!p2@Gata3!0.64!3.35!Gata3;;chr12:30213247..30213333,+!p1@Myt1l!0.64!3.35!Myt1l;;chr7:25292141..25292158,+!p2@Zfp428!0.63!13.12!Zfp428;;chr7:25292160..25292213,+!p3@Zfp428!0.63!9.21!Zfp428;;chr8:79423144..79423178,+!p3@Nr3c2!0.63!4.75!Nr3c2;;chr18:36441100..36441113,+!p3@Pura!0.63!3.91!Pura;;chr4:149611311..149611317,+!p2@Eno1!0.62!10.89!Eno1;;chr11:98603185..98603208,+!p1@Thra!0.61!221.95!Thra;;chr11:90250944..90250982,-!p2@Hlf!0.61!5.58!Hlf;;chr13:99124189..99124205,+!p1@Foxd1!0.61!5.03!Foxd1;;chr9:20385868..20385902,+!p3@Zfp846!0.61!4.75!Zfp846;;chr3:8667033..8667046,-!p3@Hey1!0.61!4.47!Hey1;;chr12:86939657..86939685,+!p6@Jdp2!0.61!3.91!Jdp2;;chr15:76352740..76352781,-!p5@Scrt1!0.61!3.07!Scrt1;;chr12:87762578..87762612,+!p1@Esrrb!0.61!3.07!Esrrb;;chr12:57714257..57714278,-!p1@Nkx2-9!0.61!3.07!Nkx2-9;;chr11:100553754..100553787,-!p1@Zfp385c!0.61!3.07!Zfp385c;;chr2:181501710..181501742,+!p2@Myt1!0.61!3.07!Myt1;;chr7:130644017..130644092,-!p1@Zkscan2!0.60!6.42!Zkscan2;;chr7:30092993..30093076,+!p1@Dpf1!0.60!5.58!Dpf1;;chr19:23216166..23216191,+!p6@Klf9!0.60!4.19!Klf9;;chr10:127896295..127896304,+!p6@Smarcc2!0.60!3.63!Smarcc2;;chr11:98636568..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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000208
 |is_obsolete=
-|library_ids=CNhs12612
+|library_id=CNhs12612!CNhs12821
+|library_id_phase_based=2:CNhs12821
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11489
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11489
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor4%252c%2520tech_rep2.CNhs12821.11489-119E4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor4%252c%2520tech_rep2.CNhs12821.11489-119E4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor4%252c%2520tech_rep2.CNhs12821.11489-119E4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor4%252c%2520tech_rep2.CNhs12821.11489-119E4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor4%252c%2520tech_rep2.CNhs12821.11489-119E4.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - substantia nigra, donor4
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12612 & CNhs12821,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.179689751831498,0,0,0,0,-0.0843392403965415,0,0,0,0,0.0534663393899805,0,-0.0849606721026137,0,0,0,0,0,0,0,0,0,0,0,0,0.448895748025511,-0.558422792324031,0,0,0,0,0,-0.112987993613846,0.155285241890633,-0.0238446060565005,0.139119199047315,0.489505371889435,0.264238928079949,0,0.106932678779961,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.0640857236970861,0,-0.0191650478653452,0,0,0,-0.1061076888152,-0.310650657339386,0.0345784209928775,-0.140687683267293,0,0,0.105522712026294,0.333440476414578,0,0,0.0852909896806329,0.193046935068067,0.436357473325513,-0.0788315948399074,0,0,0,0,0,0,0.228774121982513,0.12337041784472,0.155158600745673,0,0,0.638508823528597,0.362063355605139,0
@@ Line 61: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=119E4
+|rna_tube_id=1.19E+06
 |rna_weight_ug=10
 |sample_age=
@@ 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=table111:11489-119E4;search_select_hide=table117:11489-119E4
-|DRA_sample_Accession=CAGE@DRS008736
-|accession_numbers=DRX008846;DRR009718;DRZ001143;DRZ002528;CAGE
-|library_id=CNhs12612
 }}

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FF:11489-119E4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:04, 4 June 2020

CNhs12612

CNhs12821

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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