FF:11731-123E3: Difference between revisions

Latest revision as of 18:16, 4 June 2020

Name:	Mouse Granule cells, donor2
Species:	Mouse (Mus musculus)
Library ID:	CNhs12357
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	brain
dev stage	NA
sex	NA
age	NA
cell type	neuron, granule cell
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	RNAMG3
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		SAMD00004825

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12357		CAGE		DRX008821		DRR009693

Accession ID Mm9

Library id		BAM		CTSS
CNhs12357		DRZ001118		DRZ002503

Accession ID Mm10

Library id		BAM		CTSS
CNhs12357		DRZ012468		DRZ013853

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

CNhs12357

0	0
1	0.413
10	0
100	0.494
1000	-0.0355
1001	-0.0749
1002	0.151
1003	0.0974
1004	0
1005	-0.115
1006	0.336
1007	-0.107
1008	0
1009	-0.2
101	-0.197
1010	0
1011	0.227
1012	0
1013	-0.154
1014	0
1015	0.362
1016	0.197
1017	0
1018	0
1019	0
102	0
1020	0.562
1021	0
1022	-0.134
1023	0
1024	-0.247
1025	-0.0611
1026	0
1027	0.184
1028	0
1029	-0.176
103	-0.0848
1030	0
1031	-0.627
1032	0.211
1033	0.0032
1034	0
1035	0
1036	-0.252
1037	0
1038	0.0152
1039	-0.183
104	0
1040	-0.216
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: CNhs12357

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00349
MA0003.1	MA0003.1	0.211
MA0004.1	MA0004.1	0.569
MA0006.1	MA0006.1	0.0629
MA0007.1	MA0007.1	0.162
MA0009.1	MA0009.1	0.899
MA0014.1	MA0014.1	0.467
MA0017.1	MA0017.1	1.45937e-5
MA0018.2	MA0018.2	0.0319
MA0019.1	MA0019.1	0.387
MA0024.1	MA0024.1	0.938
MA0025.1	MA0025.1	0.568
MA0027.1	MA0027.1	0.729
MA0028.1	MA0028.1	0.279
MA0029.1	MA0029.1	0.467
MA0030.1	MA0030.1	0.378
MA0031.1	MA0031.1	0.0463
MA0035.2	MA0035.2	0.155
MA0038.1	MA0038.1	0.458
MA0039.2	MA0039.2	0.00738
MA0040.1	MA0040.1	0.548
MA0041.1	MA0041.1	0.258
MA0042.1	MA0042.1	0.472
MA0043.1	MA0043.1	0.161
MA0046.1	MA0046.1	2.42967e-7
MA0047.2	MA0047.2	4.22493e-4
MA0048.1	MA0048.1	0.252
MA0050.1	MA0050.1	3.20303e-10
MA0051.1	MA0051.1	1.9644e-5
MA0052.1	MA0052.1	0.0494
MA0055.1	MA0055.1	0.322
MA0057.1	MA0057.1	0.147
MA0058.1	MA0058.1	0.549
MA0059.1	MA0059.1	0.486
MA0060.1	MA0060.1	0.0118
MA0061.1	MA0061.1	0.0545
MA0062.2	MA0062.2	0.0184
MA0065.2	MA0065.2	3.13063e-5
MA0066.1	MA0066.1	0.207
MA0067.1	MA0067.1	0.859
MA0068.1	MA0068.1	0.589
MA0069.1	MA0069.1	0.107
MA0070.1	MA0070.1	0.495
MA0071.1	MA0071.1	0.228
MA0072.1	MA0072.1	0.205
MA0073.1	MA0073.1	0.971
MA0074.1	MA0074.1	0.425
MA0076.1	MA0076.1	0.713
MA0077.1	MA0077.1	0.007
MA0078.1	MA0078.1	0.0886
MA0079.2	MA0079.2	0.955
MA0080.2	MA0080.2	1.29088e-10
MA0081.1	MA0081.1	0.214
MA0083.1	MA0083.1	0.00362
MA0084.1	MA0084.1	0.343
MA0087.1	MA0087.1	0.609
MA0088.1	MA0088.1	0.182
MA0090.1	MA0090.1	0.00756
MA0091.1	MA0091.1	0.232
MA0092.1	MA0092.1	0.163
MA0093.1	MA0093.1	0.583
MA0099.2	MA0099.2	6.08273e-5
MA0100.1	MA0100.1	0.7
MA0101.1	MA0101.1	0.0263
MA0102.2	MA0102.2	0.84
MA0103.1	MA0103.1	0.229
MA0104.2	MA0104.2	0.521
MA0105.1	MA0105.1	0.0989
MA0106.1	MA0106.1	0.0629
MA0107.1	MA0107.1	0.0226
MA0108.2	MA0108.2	0.231
MA0111.1	MA0111.1	0.87
MA0112.2	MA0112.2	1.17131e-4
MA0113.1	MA0113.1	0.323
MA0114.1	MA0114.1	6.30025e-5
MA0115.1	MA0115.1	0.0107
MA0116.1	MA0116.1	0.131
MA0117.1	MA0117.1	0.671
MA0119.1	MA0119.1	0.0712
MA0122.1	MA0122.1	0.49
MA0124.1	MA0124.1	0.97
MA0125.1	MA0125.1	0.185
MA0131.1	MA0131.1	0.91
MA0135.1	MA0135.1	0.37
MA0136.1	MA0136.1	3.7893e-9
MA0137.2	MA0137.2	0.0162
MA0138.2	MA0138.2	0.0845
MA0139.1	MA0139.1	0.426
MA0140.1	MA0140.1	0.00273
MA0141.1	MA0141.1	0.03
MA0142.1	MA0142.1	0.0135
MA0143.1	MA0143.1	0.0113
MA0144.1	MA0144.1	0.0124
MA0145.1	MA0145.1	0.0494
MA0146.1	MA0146.1	0.039
MA0147.1	MA0147.1	0.54
MA0148.1	MA0148.1	3.02231e-6
MA0149.1	MA0149.1	0.0817
MA0150.1	MA0150.1	0.0282
MA0152.1	MA0152.1	0.0866
MA0153.1	MA0153.1	1.26413e-6
MA0154.1	MA0154.1	0.0225
MA0155.1	MA0155.1	0.795
MA0156.1	MA0156.1	1.12519e-7
MA0157.1	MA0157.1	0.0292
MA0159.1	MA0159.1	0.00311
MA0160.1	MA0160.1	0.0832
MA0162.1	MA0162.1	0.345
MA0163.1	MA0163.1	0.00525
MA0164.1	MA0164.1	0.833
MA0258.1	MA0258.1	0.0143
MA0259.1	MA0259.1	0.504

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: CNhs12357

Novel motif	Logo	P-value
1	1	0.156
10	10	0.102
100	100	0.779
101	101	0.932
102	102	0.992
103	103	0.0767
104	104	0.987
105	105	0.135
106	106	0.00469
107	107	0.0344
108	108	0.448
109	109	0.00272
11	11	0.0782
110	110	0.0938
111	111	0.101
112	112	0.00373
113	113	0.908
114	114	0.481
115	115	0.639
116	116	0.482
117	117	0.0299
118	118	0.516
119	119	0.137
12	12	0.498
120	120	0.659
121	121	0.28
122	122	0.783
123	123	0.0943
124	124	0.416
125	125	0.518
126	126	0.245
127	127	0.0462
128	128	0.0304
129	129	0.239
13	13	1.92126e-6
130	130	0.178
131	131	0.793
132	132	0.98
133	133	0.39
134	134	0.43
135	135	0.962
136	136	0.144
137	137	0.317
138	138	0.548
139	139	0.106
14	14	0.676
140	140	0.0639
141	141	0.319
142	142	0.0441
143	143	0.488
144	144	0.877
145	145	0.00936
146	146	0.369
147	147	0.711
148	148	0.406
149	149	0.212
15	15	0.157
150	150	0.11
151	151	0.451
152	152	0.0262
153	153	0.702
154	154	0.64
155	155	0.843
156	156	0.0106
157	157	0.0663
158	158	0.164
159	159	0.0356
160	160	0.331
161	161	0.481
162	162	0.708
163	163	0.421
164	164	0.0163
165	165	0.0198
166	166	0.825
167	167	0.954
168	168	0.609
169	169	0.00482
17	17	0.0198
18	18	0.449
19	19	0.0557
2	2	0.95
20	20	0.32
21	21	0.395
22	22	0.0918
23	23	0.362
24	24	0.0256
25	25	0.82
26	26	4.14059e-4
27	27	0.958
28	28	0.345
29	29	0.151
3	3	0.0777
30	30	0.663
31	31	0.849
32	32	0.523
33	33	0.165
34	34	0.557
35	35	0.381
36	36	0.487
37	37	0.0086
38	38	0.341
39	39	0.237
4	4	0.605
40	40	0.347
41	41	0.873
42	42	0.233
43	43	0.126
44	44	0.977
45	45	0.536
46	46	0.143
47	47	0.263
48	48	0.11
49	49	0.138
5	5	0.178
50	50	0.212
51	51	0.518
52	52	0.0966
53	53	0.74
54	54	0.752
55	55	0.975
56	56	0.431
57	57	0.73
58	58	0.231
59	59	0.105
6	6	0.829
60	60	0.0117
61	61	0.155
62	62	0.118
63	63	0.109
64	64	0.952
65	65	0.317
66	66	0.851
67	67	0.882
68	68	0.184
69	69	0.651
7	7	0.0151
70	70	0.0348
71	71	0.0132
72	72	0.418
73	73	0.0111
74	74	0.456
75	75	0.119
76	76	0.519
77	77	0.246
78	78	0.0256
79	79	0.688
8	8	0.125
80	80	0.977
81	81	0.787
82	82	0.202
83	83	0.158
84	84	0.685
85	85	0.191
86	86	0.228
87	87	0.192
88	88	0.337
89	89	0.382
9	9	0.261
90	90	0.217
91	91	0.284
92	92	0.284
93	93	0.0727
94	94	0.867
95	95	0.0363
96	96	0.397
97	97	0.91
98	98	0.955
99	99	0.365

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: CNhs12357

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000108 mouse granule cell 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)
0000120 (granule cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000108 (mouse granule cell 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@DRS008711
+|DRA_sample_Accession=CAGE@SAMD00004825
+|accession_numbers=CAGE;DRX008821;DRR009693;DRZ001118;DRZ002503;DRZ012468;DRZ013853
 |ancestors_in_anatomy_facet=
 |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:0000120
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr1:140739014..140739032,-!p1@Lhx9!2.04!135.42!Lhx9;;chr5:28492230..28492257,+!p1@En2!1.99!96.28!En2;;chrX:108009761..108009788,+!p1@Pou3f4!1.99!96.28!Pou3f4;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.94!108.44!Pou3f3;;chr19:55969923..55969944,+!p6@Tcf7l2!1.92!81.99!Tcf7l2;;chr12:28027561..28027591,-!p1@Sox11!1.89!475.56!Sox11;;chr14:49287186..49287225,-!p1@Otx2!1.89!76.17!Otx2;;chr9:99776566..99776612,-!p1@Sox14!1.87!73.53!Sox14;;chr16:91270004..91270023,+!p1@Olig1!1.83!76.17!Olig1;;chr3:95032091..95032183,-!p1@Mllt11!1.81!514.71!Mllt11;;chr3:101814061..101814094,+!p1@Nhlh2!1.79!60.30!Nhlh2;;chr14:104867201..104867258,-!p1@Pou4f1!1.77!80.41!Pou4f1;;chr11:84339016..84339044,-!p1@Lhx1!1.75!55.02!Lhx1;;chr7:56892217..56892221,-!p1@Dbx1!1.75!55.02!Dbx1;;chr13:72766250..72766273,+!p1@Irx2!1.74!81.99!Irx2;;chr1:19199151..19199170,+!p3@Tfap2b!1.71!50.78!Tfap2b;;chr1:19199236..19199258,+!p1@Tfap2b!1.71!49.73!Tfap2b;;chr9:91260594..91260612,-!p1@Zic1!1.71!49.73!Zic1;;chr7:116154364..116154444,+!p1@Tub!1.69!81.46!Tub;;chr9:91260616..91260653,-!p2@Zic1!1.67!45.49!Zic1;;chr17:48015839..48015915,-!p3@Foxp4!1.64!50.25!Foxp4;;chr19:55968967..55968991,+!p7@Tcf7l2!1.64!42.32!Tcf7l2;;chr12:54349410..54349461,+!p1@Npas3!1.63!50.25!Npas3;;chr12:30213247..30213333,+!p1@Myt1l!1.60!38.62!Myt1l;;chr2:151907546..151907561,+!p1@Scrt2!1.59!38.09!Scrt2;;chr4:154335024..154335039,+!p1@Hes5!1.58!44.96!Hes5;;chr5:120881900..120881914,+!p1@Lhx5!1.57!36.50!Lhx5;;chr2:28771056..28771092,-!p1@Barhl1!1.56!35.44!Barhl1;;chr1:19199119..19199134,+!p4@Tfap2b!1.56!35.44!Tfap2b;;chr7:144505957..144505972,-!p2@Ebf3!1.55!42.32!Ebf3;;chr1:19199079..19199092,+!p7@Tfap2b!1.55!34.38!Tfap2b;;chr2:79296783..79296801,-!p1@Neurod1!1.54!33.86!Neurod1;;chr9:99776617..99776631,-!p2@Sox14!1.54!33.33!Sox14;;chr2:38206580..38206600,+!p2@Lhx2!1.52!39.15!Lhx2;;chr1:19199095..19199114,+!p5@Tfap2b!1.52!32.27!Tfap2b;;chr3:66785857..66785873,-!p1@Shox2!1.52!31.74!Shox2;;chr7:30088977..30089002,+!p2@Dpf1!1.47!38.62!Dpf1;;chr2:28771380..28771413,-!p2@Barhl1!1.47!28.57!Barhl1;;chr7:144505980..144506010,-!p3@Ebf3!1.46!33.86!Ebf3;;chrX:58146612..58146615,-!p1@Sox3!1.46!28.04!Sox3;;chr7:25292331..25292421,+!p1@Zfp428!1.45!188.32!Zfp428;;chr3:127336052..127336058,+!p1@Neurog2!1.45!27.51!Neurog2;;chr11:98190918..98190951,-!p1@Neurod2!1.44!26.45!Neurod2;;chr15:76352832..76352900,-!p1@Scrt1!1.43!25.92!Scrt1;;chr12:30219426..30219506,+!p2@Myt1l!1.42!25.39!Myt1l;;chr7:144506077..144506128,-!p1@Ebf3!1.41!56.07!Ebf3;;chr2:146047829..146047847,+!p1@Insm1!1.41!43.91!Insm1;;chr10:86956396..86956411,-!p1@Ascl1!1.41!38.09!Ascl1;;chr19:55969946..55969973,+!p8@Tcf7l2!1.41!24.86!Tcf7l2;;chr1:19199221..19199234,+!p6@Tfap2b!1.41!24.86!Tfap2b;;chr14:118636214..118636235,-!p1@Sox21!1.40!29.09!Sox21;;chr3:34548909..34548927,+!p1@Sox2!1.39!39.67!Sox2;;chr2:38206744..38206766,+!p1@Lhx2!1.39!28.57!Lhx2;;chr13:56353536..56353542,-!p1@Neurog1!1.39!23.80!Neurog1;;chr1:140739042..140739054,-!p2@Lhx9!1.39!23.28!Lhx9;;chr5:106887474..106887489,-!p1@Barhl2!1.37!22.22!Barhl2;;chr4:53792566..53792578,+!p1@Tal2!1.37!22.22!Tal2;;chrX:55283799..55283813,+!p1@Zic3!1.37!22.22!Zic3;;chr13:72101141..72101158,-!p3@Irx1!1.36!27.51!Irx1;;chr4:44717334..44717367,-!p5@Pax5!1.36!21.69!Pax5;;chr4:107353376..107353452,-!p3@Dmrtb1!1.36!21.69!Dmrtb1;;chr19:59533221..59533271,+!p1@Emx2!1.35!25.92!Emx2;;chr14:118636238..118636257,-!p2@Sox21!1.35!21.16!Sox21;;chr1:19199193..19199207,+!p11@Tfap2b!1.34!20.63!Tfap2b;;chr16:91225808..91225824,+!p1@Olig2!1.34!20.63!Olig2;;chr8:12395603..12395621,+!p1@Sox1!1.34!20.63!Sox1;;chr2:65683890..65683907,+!p1@Csrnp3!1.33!38.62!Csrnp3;;chr7:30092993..30093076,+!p1@Dpf1!1.31!33.33!Dpf1;;chr13:44936126..44936164,+!p6@Jarid2!1.30!21.69!Jarid2;;chr1:19199064..19199075,+!p10@Tfap2b!1.30!19.04!Tfap2b;;chr13:72766279..72766296,+!p2@Irx2!1.29!27.51!Irx2;;chr13:72101161..72101177,-!p2@Irx1!1.29!25.39!Irx1;;chr1:122499088..122499099,+!p2@En1!1.29!18.51!En1;;chr4:13670499..13670526,+!p2@Runx1t1!1.28!39.15!Runx1t1;;chr4:139388835..139388867,-!p1@Pax7!1.28!17.99!Pax7;;chr5:140019843..140019858,+!p2@Uncx!1.28!17.99!Uncx;;chr7:91558472..91558512,-!p2@Arnt2!1.26!24.33!Arnt2;;chr3:95032197..95032208,-!p3@Mllt11!1.26!21.69!Mllt11;;chr1:122498955..122498968,+!p1@En1!1.25!16.93!En1;;chr2:70313168..70313184,+!p1@Sp5!1.24!24.33!Sp5;;chr19:55969887..55969904,+!p9@Tcf7l2!1.24!16.40!Tcf7l2;;chr15:76352677..76352737,-!p3@Scrt1!1.24!16.40!Scrt1;;chr5:148000254..148000260,+!p1@Gsx1!1.24!16.40!Gsx1;;chr5:98609885..98609900,+!p1@Prdm8!1.23!15.87!Prdm8;;chr15:76352740..76352781,-!p5@Scrt1!1.23!15.87!Scrt1;;chr2:9809357..9809371,-!p2@Gata3!1.23!15.87!Gata3;;chr4:150503457..150503498,-!p3@Camta1!1.22!17.46!Camta1;;chr2:9800207..9800234,-!p1@Gata3!1.21!46.02!Gata3;;chr5:140019865..140019886,+!p1@Uncx!1.21!15.34!Uncx;;chr13:48356475..48356492,+!p1@Id4!1.20!315.81!Id4;;chr13:72101178..72101203,-!p1@Irx1!1.20!23.28!Irx1;;chr14:122874619..122874634,+!p1@Zic2!1.20!14.81!Zic2;;chr1:19202352..19202354,+!p2@Tfap2b!1.20!14.81!Tfap2b;;chrX:108009798..108009815,+!p3@Pou3f4!1.20!14.81!Pou3f4;;chr19:55816546..55816556,+!p3@Tcf7l2!1.19!55.02!Tcf7l2;;chr13:95645580..95645598,+!p1@Otp!1.18!14.28!Otp;;chr10:84218895..84218909,+!p1@Rfx4!1.18!14.28!Rfx4;;chr1:19093112..19093124,+!p1@Tfap2d!1.17!13.75!Tfap2d;;chr2:65768174..65768247,+!p2@Csrnp3!1.17!13.75!Csrnp3;;chr15:76353005..76353021,-!p2@Scrt1!1.15!13.22!Scrt1;;chr4:22415443..22415506,-!p1@Pou3f2!1.15!13.22!Pou3f2;;chr7:25292160..25292213,+!p3@Zfp428!1.14!31.74!Zfp428;;chrX:108009734..108009752,+!p2@Pou3f4!1.14!12.70!Pou3f4;;chr1:19199021..19199048,+!p8@Tfap2b!1.14!12.70!Tfap2b;;chr4:115612528..115612533,-!p1@Dmbx1!1.14!12.70!Dmbx1;;chr4:13670571..13670625,+!p1@Runx1t1!1.13!34.38!Runx1t1;;chr3:95032184..95032195,-!p4@Mllt11!1.13!15.34!Mllt11;;chr5:106887496..106887515,-!p2@Barhl2!1.12!12.17!Barhl2;;chr11:21901608..21901634,-!p1@Otx1!1.12!12.17!Otx1;;chr5:24104751..24104773,-!p5@Smarcd3!1.10!11.64!Smarcd3;;chr3:130813200..130813252,+!p1@Lef1!1.09!50.78!Lef1;;chr7:25292310..25292329,+!p5@Zfp428!1.09!15.87!Zfp428;;chr15:40486883..40486903,+!p4@Zfpm2!1.08!14.81!Zfpm2;;chr4:129118044..129118067,-!p1@Zbtb8b!1.08!13.75!Zbtb8b;;chr14:49287107..49287125,-!p3@Otx2!1.08!11.11!Otx2;;chr9:74709695..74709722,+!p1@Onecut1!1.08!11.11!Onecut1;;chr6:55631042..55631102,-!p1@Neurod6!1.08!11.11!Neurod6;;chr1:78193687..78193692,-!p1@Pax3!1.08!11.11!Pax3;;chr7:25292141..25292158,+!p2@Zfp428!1.07!37.56!Zfp428;;chr7:91558392..91558434,-!p1@Arnt2!1.07!29.62!Arnt2;;chr5:107003725..107003746,-!p5@Zfp644!1.06!13.75!Zfp644;;chr4:13669922..13669957,+!p13@Runx1t1!1.06!10.58!Runx1t1;;chr11:33103563..33103583,-!p1@Tlx3!1.06!10.58!Tlx3;;chr19:55972441..55972456,+!p18@Tcf7l2!1.06!10.58!Tcf7l2;;chr13:29045559..29045574,-!p1@Sox4!1.05!839.51!Sox4;;chr1:189821714..189821761,+!p1@Esrrg!1.05!19.04!Esrrg;;chr2:115891534..115891589,-!p1@Meis2!1.04!141.77!Meis2;;chr4:107353508..107353547,-!p4@Dmrtb1!1.04!10.05!Dmrtb1;;chr4:22415290..22415307,-!p2@Pou3f2!1.04!10.05!Pou3f2;;chr1:170361991..170362015,-!p6@Pbx1!1.03!22.22!Pbx1;;chr2:56967334..56967366,-!p1@Nr4a2!1.03!20.10!Nr4a2;;chr3:130813736..130813752,+!p3@Lef1!1.03!13.75!Lef1;;chr11:44431016..44431045,+!p5@Ebf1!1.03!13.75!Ebf1;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!1.02!25.92!Zfhx3;;chr8:94325814..94325839,-!p2@Irx3!1.02!20.10!Irx3;;chr14:67853425..67853454,+!p1@Ebf2!1.02!13.75!Ebf2;;chr9:69608672..69608686,-!p1@Foxb1!1.02!9.52!Foxb1;;chr7:30089006..30089022,+!p3@Dpf1!1.02!9.52!Dpf1;;chr17:86020510..86020589,+!p3@Six3!1.02!9.52!Six3;;chr2:9809374..9809396,-!p4@Gata3!1.02!9.52!Gata3;;chr7:144505906..144505913,-!p7@Ebf3!1.02!9.52!Ebf3;;chr5:140019816..140019825,+!p3@Uncx!1.02!9.52!Uncx;;chr17:37140628..37140631,+!p2@Zfp57!1.01!18.51!Zfp57;;chr4:150482563..150482655,-!p2@Camta1!1.00!32.80!Camta1;;chr2:152223783..152223812,-!p4@Sox12!1.00!21.16!Sox12;;chr13:78339382..78339420,-!p3@Nr2f1!1.00!10.58!Nr2f1;;chr12:87762578..87762612,+!p1@Esrrb!1.00!8.99!Esrrb;;chr14:49282415..49282426,-!p4@Otx2!1.00!8.99!Otx2;;chr2:31495237..31495243,+!p1@Prdm12!1.00!8.99!Prdm12;;chr4:13678723..13678739,+!p10@Runx1t1!1.00!8.99!Runx1t1;;chr11:21901587..21901604,-!p2@Otx1!1.00!8.99!Otx1;;chr17:37139472..37139514,+!p1@Zfp57!0.99!60.30!Zfp57;;chr7:130644017..130644092,-!p1@Zkscan2!0.99!17.46!Zkscan2;;chr11:23978111..23978134,+!p3@Bcl11a!0.98!17.99!Bcl11a;;chr4:114730254..114730276,+!p2@Tal1!0.98!11.11!Tal1;;chr17:37139519..37139531,+!p5@Zfp57!0.98!10.05!Zfp57;;chr2:181501745..181501778,+!p1@Myt1!0.98!8.46!Myt1;;chr9:21420744..21420755,+!p3@Smarca4!0.97!24.86!Smarca4;;chr12:109242266..109242295,-!p1@Bcl11b!0.96!70.88!Bcl11b;;chr7:135019147..135019187,-!p3@Zfp668!0.96!17.99!Zfp668;;chr8:111227354..111227401,+!p@chr8:111227354..111227401,+!0.96!11.11!Zfhx3;;chr13:40826150..40826167,-!p3@Tfap2a!0.96!8.99!Tfap2a;;chr19:7342725..7342784,+!p1@Rcor2!0.95!33.33!Rcor2;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!0.95!14.28!Zfhx3;;chr2:163051181..163051205,+!p2@Tox2!0.95!7.93!Tox2;;chr4:107353563..107353590,-!p6@Dmrtb1!0.95!7.93!Dmrtb1;;chr4:122673278..122673336,+!p1@Mycl1!0.94!25.39!Mycl1;;chr9:106356211..106356242,+!p1@Pcbp4!0.93!150.76!Pcbp4;;chr7:148008023..148008092,-!p1@Zfp941!0.93!18.51!Zfp941;;chr13:78339428..78339466,-!p2@Nr2f1!0.93!10.58!Nr2f1;;chr3:34548946..34548972,+!p2@Sox2!0.93!8.46!Sox2;;chr14:67853632..67853674,+!p3@Ebf2!0.92!8.99!Ebf2;;chr12:30220074..30220102,+!p3@Myt1l!0.92!7.41!Myt1l;;chr8:80960539..80960548,-!p1@Pou4f2!0.92!7.41!Pou4f2;;chr1:140744193..140744208,-!p4@Lhx9!0.92!7.41!Lhx9;;chr1:19202185..19202187,+!p9@Tfap2b!0.92!7.41!Tfap2b;;chr1:169619683..169619694,+!p1@Lmx1a!0.92!7.41!Lmx1a;;chr19:55969687..55969714,+!p16@Tcf7l2!0.92!7.41!Tcf7l2;;chr10:84218800..84218829,+!p2@Rfx4!0.92!7.41!Rfx4;;chr7:5003205..5003234,+!p3@Zfp580!0.91!21.16!Zfp580;;chr8:90483459..90483475,-!p1@Zfp423!0.91!20.10!Zfp423;;chr11:116196664..116196679,-!p1@Foxj1!0.91!11.11!Foxj1;;chr4:124334894..124334899,+!p1@Pou3f1!0.91!9.52!Pou3f1;;chr15:100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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000108
 |is_obsolete=
-|library_ids=CNhs12357
+|library_id=CNhs12357
+|library_id_phase_based=2:CNhs12357
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11731
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11731
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor2.CNhs12357.11731-123E3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor2.CNhs12357.11731-123E3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor2.CNhs12357.11731-123E3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor2.CNhs12357.11731-123E3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor2.CNhs12357.11731-123E3.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Granule cells, donor2
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12357,LSID913,release011,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0886003464642375,0,0,0,0,0,-0.380701426632628,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.121548212284802,0,0,0,0,0,0,0,0,0,0,0,0,0.669604279082846,-0.244981229156655,0,0,0,0,0,-0.117120263909331,0.18440492317299,-0.285876361156759,0.589824273933687,0.99628546962699,0.672369147627484,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0,0,-0.110239959110685,-0.310650657339386,0.155350520396294,-0.0365927089968535,0,0,0.0901656330935525,0.18440492317299,0,0,0.0648417018248107,0.161037658669614,0.426176714735498,-0.0788315948399074,0,0,0,0,0,0,0.104614816243968,0.0674409401674345,-0.023006792285091,0,0,0,0.453192152750925,0
@@ Line 61: / Line 73: @@
 |rna_rin=
 |rna_sample_type=total RNA
-|rna_tube_id=123E3
+|rna_tube_id=1.23E+05
 |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=table111:11731-123E3;search_select_hide=table117:11731-123E3
-|DRA_sample_Accession=CAGE@DRS008711
-|accession_numbers=DRX008821;DRR009693;DRZ001118;DRZ002503;CAGE
-|library_id=CNhs12357
 }}

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FF:11731-123E3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:16, 4 June 2020

CNhs12357

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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