FF:12460-132E3: Difference between revisions

Latest revision as of 18:39, 4 June 2020

Name:	ST2 (Mesenchymal stem cells) cells, medium change (without induction)
Species:	Mouse (Mus musculus)
Library ID:	CNhs13275
Sample type:	time courses
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	bone marrow
dev stage	NA
sex	NA
age	NA
cell type	mesenchymal stem cell
cell line	ST2
company	NA
collaboration	Yasushi Okazaki (Saitama medical college)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

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

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005712

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13275		CAGE		DRX008906		DRR009780

Accession ID Mm9

Library id		BAM		CTSS
CNhs13275		DRZ001205		DRZ002588

Accession ID Mm10

Library id		BAM		CTSS
CNhs13275		DRZ012555		DRZ013938

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

CNhs13275

0	0
1	0
10	0
100	0
1000	0.236
1001	-0.0631
1002	-0.0655
1003	0.173
1004	0
1005	0
1006	-0.142
1007	-0.0401
1008	0
1009	0.653
101	-0.024
1010	0
1011	-0.237
1012	0
1013	0.0697
1014	-0.0851
1015	0.171
1016	0.113
1017	0
1018	0
1019	0
102	0
1020	0.1
1021	0.182
1022	-0.124
1023	0
1024	-0.307
1025	0
1026	0
1027	-0.048
1028	0.1
1029	-0.176
103	0.45
1030	0
1031	-0.446
1032	-0.167
1033	0.1
1034	0
1035	0
1036	0.179
1037	0
1038	0.0302
1039	-0.0646
104	0
1040	0.31
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: CNhs13275

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.187
MA0003.1	MA0003.1	0.713
MA0004.1	MA0004.1	0.432
MA0006.1	MA0006.1	0.567
MA0007.1	MA0007.1	0.698
MA0009.1	MA0009.1	0.779
MA0014.1	MA0014.1	0.242
MA0017.1	MA0017.1	0.482
MA0018.2	MA0018.2	0.1
MA0019.1	MA0019.1	0.885
MA0024.1	MA0024.1	0.288
MA0025.1	MA0025.1	0.763
MA0027.1	MA0027.1	0.35
MA0028.1	MA0028.1	0.00164
MA0029.1	MA0029.1	0.52
MA0030.1	MA0030.1	0.267
MA0031.1	MA0031.1	0.376
MA0035.2	MA0035.2	0.00311
MA0038.1	MA0038.1	0.737
MA0039.2	MA0039.2	0.924
MA0040.1	MA0040.1	0.263
MA0041.1	MA0041.1	0.706
MA0042.1	MA0042.1	0.236
MA0043.1	MA0043.1	0.672
MA0046.1	MA0046.1	6.82727e-8
MA0047.2	MA0047.2	0.24
MA0048.1	MA0048.1	8.77558e-4
MA0050.1	MA0050.1	0.752
MA0051.1	MA0051.1	0.992
MA0052.1	MA0052.1	2.9933e-4
MA0055.1	MA0055.1	6.42822e-5
MA0057.1	MA0057.1	0.204
MA0058.1	MA0058.1	0.155
MA0059.1	MA0059.1	0.165
MA0060.1	MA0060.1	0.0236
MA0061.1	MA0061.1	0.264
MA0062.2	MA0062.2	4.92563e-4
MA0065.2	MA0065.2	0.109
MA0066.1	MA0066.1	0.242
MA0067.1	MA0067.1	0.997
MA0068.1	MA0068.1	0.749
MA0069.1	MA0069.1	0.522
MA0070.1	MA0070.1	0.17
MA0071.1	MA0071.1	0.55
MA0072.1	MA0072.1	0.879
MA0073.1	MA0073.1	0.576
MA0074.1	MA0074.1	0.897
MA0076.1	MA0076.1	0.00316
MA0077.1	MA0077.1	0.521
MA0078.1	MA0078.1	0.17
MA0079.2	MA0079.2	0.0834
MA0080.2	MA0080.2	0.0674
MA0081.1	MA0081.1	0.482
MA0083.1	MA0083.1	0.00283
MA0084.1	MA0084.1	0.458
MA0087.1	MA0087.1	0.75
MA0088.1	MA0088.1	0.00398
MA0090.1	MA0090.1	0.101
MA0091.1	MA0091.1	0.412
MA0092.1	MA0092.1	0.204
MA0093.1	MA0093.1	0.431
MA0099.2	MA0099.2	5.68978e-5
MA0100.1	MA0100.1	0.149
MA0101.1	MA0101.1	0.456
MA0102.2	MA0102.2	0.401
MA0103.1	MA0103.1	1.92649e-4
MA0104.2	MA0104.2	0.988
MA0105.1	MA0105.1	0.0171
MA0106.1	MA0106.1	0.00156
MA0107.1	MA0107.1	0.892
MA0108.2	MA0108.2	0.0194
MA0111.1	MA0111.1	0.335
MA0112.2	MA0112.2	0.00476
MA0113.1	MA0113.1	0.983
MA0114.1	MA0114.1	0.938
MA0115.1	MA0115.1	0.461
MA0116.1	MA0116.1	0.0288
MA0117.1	MA0117.1	0.556
MA0119.1	MA0119.1	0.307
MA0122.1	MA0122.1	0.68
MA0124.1	MA0124.1	0.454
MA0125.1	MA0125.1	0.00295
MA0131.1	MA0131.1	0.576
MA0135.1	MA0135.1	0.0307
MA0136.1	MA0136.1	0.92
MA0137.2	MA0137.2	0.0518
MA0138.2	MA0138.2	0.00141
MA0139.1	MA0139.1	0.479
MA0140.1	MA0140.1	2.04701e-4
MA0141.1	MA0141.1	0.166
MA0142.1	MA0142.1	0.178
MA0143.1	MA0143.1	0.783
MA0144.1	MA0144.1	0.0887
MA0145.1	MA0145.1	0.379
MA0146.1	MA0146.1	0.0113
MA0147.1	MA0147.1	0.88
MA0148.1	MA0148.1	0.553
MA0149.1	MA0149.1	0.0481
MA0150.1	MA0150.1	0.231
MA0152.1	MA0152.1	0.04
MA0153.1	MA0153.1	2.50664e-5
MA0154.1	MA0154.1	0.212
MA0155.1	MA0155.1	0.952
MA0156.1	MA0156.1	0.999
MA0157.1	MA0157.1	0.774
MA0159.1	MA0159.1	0.266
MA0160.1	MA0160.1	0.673
MA0162.1	MA0162.1	0.0601
MA0163.1	MA0163.1	0.0184
MA0164.1	MA0164.1	0.335
MA0258.1	MA0258.1	0.232
MA0259.1	MA0259.1	0.346

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: CNhs13275

Novel motif	Logo	P-value
1	1	0.206
10	10	0.0123
100	100	0.63
101	101	0.235
102	102	0.188
103	103	0.0729
104	104	0.708
105	105	0.886
106	106	0.542
107	107	0.74
108	108	0.543
109	109	0.0248
11	11	0.0774
110	110	0.0194
111	111	0.501
112	112	0.427
113	113	0.118
114	114	0.444
115	115	0.689
116	116	0.0351
117	117	8.12752e-4
118	118	0.843
119	119	0.242
12	12	0.66
120	120	0.211
121	121	0.778
122	122	0.147
123	123	0.312
124	124	0.145
125	125	0.195
126	126	0.34
127	127	0.137
128	128	0.657
129	129	0.701
13	13	0.00555
130	130	0.779
131	131	0.527
132	132	0.35
133	133	0.163
134	134	0.516
135	135	0.188
136	136	0.563
137	137	0.538
138	138	0.81
139	139	0.349
14	14	0.503
140	140	0.922
141	141	0.797
142	142	0.814
143	143	0.0897
144	144	0.159
145	145	0.102
146	146	0.443
147	147	0.907
148	148	0.543
149	149	0.199
15	15	0.864
150	150	0.0358
151	151	0.973
152	152	0.126
153	153	0.921
154	154	0.411
155	155	0.206
156	156	4.29054e-38
157	157	0.823
158	158	0.415
159	159	0.124
160	160	0.595
161	161	0.376
162	162	0.901
163	163	0.598
164	164	0.00508
165	165	0.962
166	166	0.764
167	167	0.301
168	168	0.411
169	169	0.00264
17	17	0.15
18	18	0.228
19	19	0.316
2	2	0.421
20	20	0.0373
21	21	0.0336
22	22	0.32
23	23	0.129
24	24	0.706
25	25	0.868
26	26	0.0228
27	27	0.39
28	28	0.691
29	29	0.00394
3	3	0.0826
30	30	0.451
31	31	0.625
32	32	0.344
33	33	0.17
34	34	0.657
35	35	0.683
36	36	0.0261
37	37	0.0118
38	38	0.715
39	39	0.489
4	4	0.757
40	40	0.36
41	41	0.4
42	42	0.366
43	43	0.514
44	44	0.176
45	45	0.574
46	46	0.341
47	47	0.138
48	48	0.265
49	49	0.869
5	5	0.185
50	50	0.72
51	51	0.935
52	52	0.689
53	53	0.379
54	54	0.57
55	55	0.378
56	56	0.773
57	57	0.107
58	58	0.902
59	59	0.242
6	6	0.933
60	60	0.358
61	61	0.627
62	62	0.399
63	63	0.549
64	64	0.584
65	65	0.925
66	66	0.636
67	67	0.966
68	68	0.691
69	69	0.487
7	7	0.315
70	70	0.00285
71	71	0.00104
72	72	0.954
73	73	0.0189
74	74	0.735
75	75	0.0383
76	76	0.204
77	77	0.38
78	78	0.025
79	79	0.732
8	8	0.0824
80	80	0.0473
81	81	0.698
82	82	0.518
83	83	0.502
84	84	0.927
85	85	0.653
86	86	0.572
87	87	0.0823
88	88	0.711
89	89	0.783
9	9	0.959
90	90	0.0226
91	91	0.337
92	92	0.678
93	93	0.205
94	94	0.835
95	95	0.0439
96	96	0.415
97	97	0.661
98	98	0.402
99	99	0.748

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: CNhs13275

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000488 mouse ST2 Mesenchymal stem cells, cells 0hr after medium change , without induction 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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000034 (stem cell)

UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000404 (mouse mesenchymal stem cell line: ST2 sample)
0000333 (medium change sample)
0000357 (0 hr sample)
0000488 (mouse ST2 Mesenchymal stem cells, cells 0hr after medium change , without induction 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:0000134 (mesenchymal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008769
+|DRA_sample_Accession=CAGE@SAMD00005712
-|accession_numbers=CAGE;DRX008906;DRR009780;DRZ001205;DRZ002588
+|accession_numbers=CAGE;DRX008906;DRR009780;DRZ001205;DRZ002588;DRZ012555;DRZ013938
 |ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0000548,CL:0002320,CL:0002371,CL:0000219,CL:0000134,CL:0000255,CL:0000034
@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
+|donor=biol_rep2
 |expression_enrichment_score=chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.90!97.94!Zbtb11;;chr15:102828658..102828678,+!p1@Hoxc6!1.85!70.14!Hoxc6;;chr19:5447886..5447905,+!p1@Fosl1!1.73!53.00!Fosl1;;chr6:52190467..52190500,-!p1@Hoxa10!1.65!43.38!Hoxa10;;chr2:30700857..30700873,+!p3@Prrx2!1.60!52.74!Prrx2;;chr12:74147689..74147711,-!p1@Six1!1.58!79.75!Six1;;chr2:30700881..30700916,+!p1@Prrx2!1.57!67.28!Prrx2;;chr3:99057269..99057306,+!p1@Tbx15!1.56!42.86!Tbx15;;chr15:102797288..102797302,+!p1@Hoxc10!1.49!29.62!Hoxc10;;chr16:14705961..14705978,+!p2@Snai2!1.45!121.84!Snai2;;chr19:5447692..5447711,+!p2@Fosl1!1.45!27.28!Fosl1;;chr17:44951553..44951586,-!p2@Runx2!1.44!29.10!Runx2;;chr16:14705925..14705951,+!p1@Snai2!1.42!170.68!Snai2;;chr6:83661226..83661282,+!p1@Vax2!1.32!20.00!Vax2;;chr15:102751578..102751600,+!p2@Hoxc13!1.32!20.00!Hoxc13;;chr13:99124189..99124205,+!p1@Foxd1!1.30!28.32!Foxd1;;chr6:52176164..52176195,-!p1@Hoxa9!1.28!22.34!Hoxa9;;chr15:102751603..102751630,+!p1@Hoxc13!1.27!17.67!Hoxc13;;chr13:31898729..31898761,+!p1@Foxc1!1.26!42.09!Foxc1;;chr15:102797225..102797243,+!p2@Hoxc10!1.26!17.41!Hoxc10;;chr13:55932591..55932622,-!p1@Pitx1!1.22!18.70!Pitx1;;chr2:152758901..152758925,-!p1@Foxs1!1.21!67.28!Foxs1;;chr6:6831986..6832007,-!p4@Dlx5!1.21!15.33!Dlx5;;chr13:72766250..72766273,+!p1@Irx2!1.18!21.82!Irx2;;chr6:6831950..6831985,-!p2@Dlx5!1.18!15.59!Dlx5;;chr15:102797170..102797182,+!p3@Hoxc10!1.15!12.99!Hoxc10;;chr13:31898637..31898653,+!p2@Foxc1!1.10!20.52!Foxc1;;chr8:94881733..94881790,+!p1@Irx5!1.09!22.34!Irx5;;chr15:102797183..102797205,+!p4@Hoxc10!1.09!11.17!Hoxc10;;chr13:31898496..31898519,+!p3@Foxc1!1.08!17.93!Foxc1;;chr9:87626083..87626108,-!p1@Tbx18!1.04!22.08!Tbx18;;chr7:52071956..52071978,-!p1@Atf5!1.02!306.81!Atf5;;chr12:34642682..34642753,+!p2@Twist1!1.02!25.72!Twist1;;chr9:87625971..87625992,-!p2@Tbx18!1.00!9.09!Tbx18;;chr15:102087737..102087801,-!p3@Rarg!0.99!14.81!Rarg;;chr1:165243792..165243808,-!p1@Prrx1!0.98!30.39!Prrx1;;chr15:102828642..102828653,+!p2@Hoxc6!0.98!8.57!Hoxc6;;chr2:30700788..30700824,+!p2@Prrx2!0.97!12.99!Prrx2;;chr6:6832076..6832092,-!p1@Dlx5!0.97!9.87!Dlx5;;chr15:102839948..102839975,+!p3@Hoxc6!0.96!8.05!Hoxc6;;chr15:97738692..97738747,-!p1@Vdr!0.95!44.42!Vdr;;chr1:186556410..186556424,-!p1@Hlx!0.94!24.94!Hlx;;chr11:96153767..96153822,+!p1@Hoxb6!0.93!11.95!Hoxb6;;chr10:67375368..67375433,-!p1@Zfp365!0.90!12.47!Zfp365;;chr16:14705668..14705683,+!p3@Snai2!0.90!7.01!Snai2;;chr3:99057256..99057268,+!p3@Tbx15!0.90!7.01!Tbx15;;chr19:55816546..55816556,+!p3@Tcf7l2!0.89!27.02!Tcf7l2;;chr13:55932624..55932641,-!p2@Pitx1!0.89!6.75!Pitx1;;chr13:72101178..72101203,-!p1@Irx1!0.88!10.39!Irx1;;chr15:102751552..102751563,+!p3@Hoxc13!0.87!6.49!Hoxc13;;chr10:67000609..67000625,+!p1@Egr2!0.85!14.81!Egr2;;chr6:52163319..52163342,-!p1@Hoxa3!0.85!9.09!Hoxa3;;chr16:14705746..14705761,+!p4@Snai2!0.84!5.98!Snai2;;chr19:5424822..5424845,-!p3@Drap1!0.82!23.64!Drap1;;chr1:140739014..140739032,-!p1@Lhx9!0.82!7.27!Lhx9;;chr13:55932739..55932756,-!p5@Pitx1!0.81!5.46!Pitx1;;chr2:167363692..167363710,+!p1@Snai1!0.79!69.10!Snai1;;chr15:102839976..102839989,+!p4@Hoxc6!0.79!5.20!Hoxc6;;chr6:72185232..72185272,-!p1@Atoh8!0.78!15.59!Atoh8;;chr1:165243272..165243283,-!p6@Prrx1!0.78!6.23!Prrx1;;chr3:5218629..5218684,+!p1@Zfhx4!0.76!16.89!Zfhx4;;chr12:86940338..86940357,+!p1@Jdp2!0.75!50.66!Jdp2;;chr2:30701003..30701028,+!p6@Prrx2!0.75!4.68!Prrx2;;chr10:80811972..80811985,-!p8@Hmg20b!0.75!4.68!Hmg20b;;chr5:65203599..65203617,+!p8@Klf3!0.73!7.53!Klf3;;chr6:52190668..52190682,-!p3@Hoxa10!0.73!4.42!Hoxa10;;chr1:93698030..93698064,+!p1@Twist2!0.71!8.83!Twist2;;chr2:152758938..152758954,-!p2@Foxs1!0.71!5.98!Foxs1;;chr3:66785181..66785199,-!p2@Shox2!0.71!4.16!Shox2;;chr6:52176144..52176161,-!p2@Hoxa9!0.71!4.16!Hoxa9;;chr13:31717548..31717596,+!p1@Foxf2!0.69!8.31!Foxf2;;chr8:123640063..123640077,+!p1@Foxc2!0.69!7.53!Foxc2;;chr15:102820964..102821006,+!p1@Hoxc8!0.69!3.90!Hoxc8;;chr12:120085700..120085711,+!p1@Sp8!0.69!3.90!Sp8;;chr4:134676555..134676575,+!p2@Runx3!0.69!3.90!Runx3;;chr19:5423800..5423821,-!p5@Drap1!0.68!5.98!Drap1;;chr4:135699731..135699747,+!p1@Id3!0.66!470.99!Id3;;chr9:96653072..96653154,-!p1@Zbtb38!0.66!10.65!Zbtb38;;chr8:94325321..94325366,-!p1@Irx3!0.66!9.61!Irx3;;chr7:144506077..144506128,-!p1@Ebf3!0.66!9.09!Ebf3;;chr11:94981424..94981439,+!p1@Dlx3!0.66!4.16!Dlx3;;chr10:80889867..80889924,-!p1@Nfic!0.65!115.09!Nfic;;chr15:102076870..102076941,-!p1@Rarg!0.65!44.16!Rarg;;chr11:44430812..44430838,+!p1@Ebf1!0.65!38.97!Ebf1;;chr15:102087880..102087927,-!p2@Rarg!0.65!8.83!Rarg;;chr12:9581284..9581303,+!p2@Osr1!0.65!7.27!Osr1;;chr1:165243591..165243625,-!p2@Prrx1!0.65!5.72!Prrx1;;chr19:28754692..28754757,-!p1@Glis3!0.64!16.11!Glis3;;chr4:149611832..149611846,+!p3@LOC100045967,p3@LOC100503183,p4@Eno1,p4@Gm5506!0.64!3.38!Eno1;;chr7:35904304..35904320,+!p1@Cebpa!0.63!79.23!Cebpa;;chr5:53981592..53981616,+!p3@Rbpj!0.63!6.75!Rbpj;;chr6:72185210..72185228,-!p3@Atoh8!0.63!5.98!Atoh8;;chr12:34642510..34642530,+!p1@Twist1!0.62!11.69!Twist1;;chr19:5424768..5424811,-!p2@Drap1!0.61!70.14!Drap1;;chr1:165243379..165243402,-!p3@Prrx1!0.61!4.94!Prrx1;;chr1:165243653..165243664,-!p4@Prrx1!0.61!4.68!Prrx1;;chr7:52960730..52960762,+!p3@Dbp!0.61!4.16!Dbp;;chr1:165243638..165243649,-!p5@Prrx1!0.61!3.90!Prrx1;;chr13:31898529..31898542,+!p5@Foxc1!0.61!3.90!Foxc1;;chr6:52184901..52184959,-!p2@Hoxa10!0.61!3.12!Hoxa10;;chr2:30700830..30700843,+!p4@Prrx2!0.61!3.12!Prrx2;;chr16:4594740..4594759,+!p1@Glis2!0.60!41.05!Glis2;;chr8:94325814..94325839,-!p2@Irx3!0.60!7.01!Irx3;;chr13:31898767..31898785,+!p4@Foxc1!0.59!3.64!Foxc1;;chr13:99124236..99124243,+!p2@Foxd1!0.59!2.86!Foxd1;;chr13:72766234..72766243,+!p3@Irx2!0.59!2.86!Irx2;;chr17:44951431..44951445,-!p3@Runx2!0.59!2.86!Runx2;;chr6:6831928..6831949,-!p3@Dlx5!0.59!2.86!Dlx5;;chr3:66785201..66785226,-!p3@Shox2!0.59!2.86!Shox2;;chr17:34784073..34784118,+!p2@Atf6b!0.57!13.25!Atf6b;;chr1:186556375..186556404,-!p3@Hlx!0.57!5.46!Hlx;;chr1:57029281..57029326,-!p1@Satb2!0.57!4.68!Satb2;;chr6:72185179..72185196,-!p4@Atoh8!0.57!3.90!Atoh8;;chr8:123640090..123640101,+!p2@Foxc2!0.57!3.12!Foxc2;;chr12:9581262..9581282,+!p1@Osr1!0.56!38.97!Osr1;;chr15:76287876..76287894,+!p1@Scx!0.56!17.67!Scx;;chr19:46380235..46380277,+!p3@Nfkb2!0.56!6.49!Nfkb2;;chr16:92697354..92697362,-!p3@Runx1!0.56!4.42!Runx1;;chr11:100720767..100720797,+!p4@Stat5a!0.56!2.60!Stat5a;;chr10:126727842..126727859,+!p1@Ddit3!0.55!93.00!Ddit3;;chr13:55431084..55431137,-!p1@Mxd3!0.55!24.42!Mxd3;;chr1:93698068..93698085,+!p2@Twist2!0.55!3.12!Twist2;;chr16:55966451..55966484,+!p3@Rpl24,p3@Zbtb11!0.54!17.93!Zbtb11;;chr9:63869751..63869767,-!p1@Smad6!0.54!7.79!Smad6;;chr9:87625998..87626007,-!p4@Tbx18!0.52!2.34!Tbx18;;chr17:44951598..44951609,-!p12@Runx2!0.52!2.34!Runx2;;chr1:186556495..186556506,-!p8@Hlx!0.52!2.34!Hlx;;chr3:66785857..66785873,-!p1@Shox2!0.52!2.34!Shox2;;chr13:31717775..31717788,+!p4@Foxf2!0.52!2.34!Foxf2;;chr12:74147860..74147888,-!p2@Six1!0.52!2.34!Six1;;chr11:98603160..98603171,+!p3@Thra!0.51!13.25!Thra;;chr11:44431687..44431706,+!p2@Ebf1!0.51!13.25!Ebf1;;chr13:72101161..72101177,-!p2@Irx1!0.51!3.38!Irx1;;chr7:144505980..144506010,-!p3@Ebf3!0.51!2.86!Ebf3;;chr15:75578637..75578669,-!p2@Mafa!0.51!2.60!Mafa;;chr13:53568104..53568156,-!p1@Msx2!0.50!3.64!Msx2;;chr13:72766279..72766296,+!p2@Irx2!0.50!3.64!Irx2;;chr11:96145450..96145517,+!p2@Hoxb7!0.50!3.64!Hoxb7;;chr17:35653725..35653780,-!p1@Tcf19!0.49!47.28!Tcf19;;chr19:46380172..46380231,+!p2@Nfkb2!0.49!18.96!Nfkb2;;chr7:105851808..105851822,+!p3@Prkrir!0.49!9.35!Prkrir;;chr15:102076652..102076679,-!p4@Rarg!0.49!4.42!Rarg;;chr3:5218590..5218614,+!p3@Zfhx4!0.49!4.16!Zfhx4;;chr2:71367871..71367898,+!p1@Dlx1!0.49!2.08!Dlx1;;chr19:5447859..5447866,+!p3@Fosl1!0.49!2.08!Fosl1;;chr15:102751568..102751573,+!p4@Hoxc13!0.49!2.08!Hoxc13;;chr19:59534008..59534046,+!p7@Emx2!0.49!2.08!Emx2;;chr19:5424878..5424890,-!p7@Drap1!0.48!3.64!Drap1;;chr13:72101141..72101158,-!p3@Irx1!0.47!2.60!Irx1;;chr1:186556323..186556370,-!p2@Hlx!0.46!6.49!Hlx;;chr10:119913278..119913298,-!p2@Hmga2!0.46!5.20!Hmga2;;chr11:5761979..5761992,+!p2@Aebp1!0.46!4.68!Aebp1;;chr6:115311030..115311065,+!p4@Pparg!0.46!3.12!Pparg;;chr8:94881872..94881887,+!p2@Irx5!0.46!2.08!Irx5;;chr9:106356211..106356242,+!p1@Pcbp4!0.45!49.62!Pcbp4;;chr16:43363152..43363186,+!p3@Zbtb20!0.45!5.20!Zbtb20;;chr19:28754655..28754673,-!p3@Glis3!0.45!3.12!Glis3;;chrX:137077636..137077647,-!p7@Tsc22d3!0.45!2.34!Tsc22d3;;chr2:38206744..38206766,+!p1@Lhx2!0.45!2.34!Lhx2;;chr1:57028556..57028583,-!p5@Satb2!0.45!1.82!Satb2;;chr1:57028538..57028553,-!p6@Satb2!0.45!1.82!Satb2;;chr12:74147842..74147856,-!p3@Six1!0.45!1.82!Six1;;chr17:44873599..44873623,-!p7@Runx2!0.45!1.82!Runx2;;chr16:92697560..92697592,-!p2@Runx1!0.44!15.07!Runx1;;chrX:137077653..137077669,-!p3@Tsc22d3!0.44!10.65!Tsc22d3;;chr17:33766353..33766393,+!p2@Zfp414!0.44!6.23!Zfp414;;chr6:72739034..72739055,-!p3@Tcf7l1!0.44!4.68!Tcf7l1;;chr6:115310872..115310899,+!p2@Pparg!0.44!3.64!Pparg;;chr12:9581317..9581333,+!p3@Osr1!0.44!3.12!Osr1;;chr7:133839456..133839523,+!p1@Bola2!0.43!122.10!Bola2;;chr12:86940300..86940312,+!p2@Jdp2!0.43!5.20!Jdp2;;chr5:53981692..53981768,+!p2@Rbpj!0.42!42.86!Rbpj;;chr6:117791192..117791269,+!p1@Zfp637!0.42!37.93!Zfp637;;chr15:81977802..81977828,+!p2@Srebf2!0.42!20.00!Srebf2;;chr10:119913310..119913366,-!p1@Hmga2!0.42!18.19!Hmga2;;chrX:7339938..7339963,+!p1@Tfe3!0.42!11.43!Tfe3;;chr5:24107993..24108036,-!p2@Smarcd3!0.42!4.94!Smarcd3;;chrX:7341077..7341091,+!p5@Tfe3!0.42!3.38!Tfe3;;chr3:5218516..5218544,+!p2@Zfhx4!0.42!2.86!Zfhx4;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.42!2.60!Carhsp1;;chr12:9581243..9581254,+!p4@Osr1!0.42!2.60!Osr1;;chr18:83079981..83080037,+!p6@Zfp516!0.41!3.38!Zfp516;;chr10:67375146..67375208,-!p2@Zfp365!0.41!2.86!Zfp365;;chr11:44431016..44431045,+!p5@Ebf1!0.41!2.60!Ebf1;;chr16:25865862..25865871,+!p8@Trp63!0.41!1.56!Trp63;;chr3:99044284..99044308,+!p4@Tbx15!0.41!1.56!Tbx15;;chr15:102821007..102821021,+!p2@Hoxc8!0.41!1.56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 |ffid_belonging_in_development=CL:0000134
@@ Line 45: / Line 46: @@
 |is_obsolete=
 |library_id=CNhs13275
-|library_id_phase_based=1:CNhs13275
+|library_id_phase_based=2:CNhs13275
-|name=ST2 (Mesenchymal stem cells) cells, medium change (without induction), 00hr, biol_rep2 (000hC5)
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12460
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12460
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/ST2%2520%2528Mesenchymal%2520stem%2520cells%2529%2520cells%252c%2520medium%2520change%2520%2528without%2520induction%2529%252c%252000hr%252c%2520biol_rep2%2520%2528000hC5%2529.CNhs13275.12460-132E3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/ST2%2520%2528Mesenchymal%2520stem%2520cells%2529%2520cells%252c%2520medium%2520change%2520%2528without%2520induction%2529%252c%252000hr%252c%2520biol_rep2%2520%2528000hC5%2529.CNhs13275.12460-132E3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/ST2%2520%2528Mesenchymal%2520stem%2520cells%2529%2520cells%252c%2520medium%2520change%2520%2528without%2520induction%2529%252c%252000hr%252c%2520biol_rep2%2520%2528000hC5%2529.CNhs13275.12460-132E3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/ST2%2520%2528Mesenchymal%2520stem%2520cells%2529%2520cells%252c%2520medium%2520change%2520%2528without%2520induction%2529%252c%252000hr%252c%2520biol_rep2%2520%2528000hC5%2529.CNhs13275.12460-132E3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/ST2%2520%2528Mesenchymal%2520stem%2520cells%2529%2520cells%252c%2520medium%2520change%2520%2528without%2520induction%2529%252c%252000hr%252c%2520biol_rep2%2520%2528000hC5%2529.CNhs13275.12460-132E3.mm9.nobarcode.rdna.fa.gz
+|name=ST2 (Mesenchymal stem cells) cells, medium change (without induction)
 |namespace=FANTOM5
 |part_of=
 |profile_cagescan=,,,
 |profile_hcage=CNhs13275,LSID1020,release013,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.0676472066836305,0,0,0,0,0,0.126817569578848,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.010172065709981,0,0,0,0,0,0.792091789135453,0,0,0,0,0,0,0.050148389656749,-0.458126013010533,0,0,0,0,0,-0.0340426665249007,-0.130097694438766,-0.390138951848876,-0.984211366477826,-0.269868638010351,0.100296779313498,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0.163606451471254,0.250263338628353,0.361525752008184,0,-0.0679457192233448,-0.310650657339386,-0.158091042771083,-0.0365927089968535,0,-0.0780086007519514,-0.107177024667156,-0.121484695258618,0,0,-0.0831454278865671,-0.245311440353327,0.263515497613207,-0.0788315948399074,0,0,0,0,0,0,0.220864979371337,0.358742290496493,0.64961589598897,0,0,0.100296779313498,0.100296779313498,0
@@ Line 64: / Line 74: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=132E3
+|rna_tube_id=1.32E+05
-|rna_weight_ug=5.50
+|rna_weight_ug=5.5
 |sample_age=
 |sample_category=time courses
@@ Line 86: / Line 96: @@
 |sample_strain=
 |sample_tissue=bone marrow
+|time=00hr
+|timecourse=MSC_to_adipocyte_(mouse),MSC_to_osteocyte_(mouse)
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12460-132E3;search_select_hide=table117:12460-132E3
 }}

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FF:12460-132E3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:39, 4 June 2020

CNhs13275

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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