FF:11718-123C8: Difference between revisions

Latest revision as of 18:16, 4 June 2020

Name:	Mouse Microglia, donor1
Species:	Mouse (Mus musculus)
Library ID:	CNhs12629
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	microglial 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	RNAMG1
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005195

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12629		CAGE		DRX008828		DRR009700

Accession ID Mm9

Library id		BAM		CTSS
CNhs12629		DRZ001125		DRZ002510

Accession ID Mm10

Library id		BAM		CTSS
CNhs12629		DRZ012475		DRZ013860

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

CNhs12629

0	0
1	0
10	0
100	0
1000	0.527
1001	-0.0749
1002	0.09
1003	0.314
1004	0
1005	0
1006	0.112
1007	-0.183
1008	0
1009	-0.0558
101	-0.611
1010	0
1011	0.00496
1012	0
1013	0.1
1014	-0.0874
1015	0.122
1016	0.381
1017	0
1018	0
1019	0
102	0
1020	0.491
1021	0.135
1022	-0.0704
1023	0
1024	-0.14
1025	0
1026	0
1027	0.114
1028	0
1029	-0.176
103	0.398
1030	0
1031	0.489
1032	0.523
1033	-0.0665
1034	0
1035	0
1036	-0.158
1037	0
1038	-0.0473
1039	0.0325
104	0
1040	0.275
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: CNhs12629

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0571
MA0003.1	MA0003.1	0.112
MA0004.1	MA0004.1	0.727
MA0006.1	MA0006.1	0.369
MA0007.1	MA0007.1	0.513
MA0009.1	MA0009.1	0.115
MA0014.1	MA0014.1	0.724
MA0017.1	MA0017.1	0.0502
MA0018.2	MA0018.2	0.0496
MA0019.1	MA0019.1	0.305
MA0024.1	MA0024.1	4.70811e-4
MA0025.1	MA0025.1	0.681
MA0027.1	MA0027.1	0.824
MA0028.1	MA0028.1	8.53097e-6
MA0029.1	MA0029.1	0.82
MA0030.1	MA0030.1	0.254
MA0031.1	MA0031.1	0.235
MA0035.2	MA0035.2	0.00289
MA0038.1	MA0038.1	0.00331
MA0039.2	MA0039.2	0.696
MA0040.1	MA0040.1	0.515
MA0041.1	MA0041.1	0.266
MA0042.1	MA0042.1	0.677
MA0043.1	MA0043.1	0.0868
MA0046.1	MA0046.1	6.89682e-8
MA0047.2	MA0047.2	0.0512
MA0048.1	MA0048.1	0.691
MA0050.1	MA0050.1	0.7
MA0051.1	MA0051.1	0.936
MA0052.1	MA0052.1	0.571
MA0055.1	MA0055.1	0.347
MA0057.1	MA0057.1	0.771
MA0058.1	MA0058.1	0.878
MA0059.1	MA0059.1	0.684
MA0060.1	MA0060.1	7.77625e-4
MA0061.1	MA0061.1	0.193
MA0062.2	MA0062.2	1.32951e-7
MA0065.2	MA0065.2	0.47
MA0066.1	MA0066.1	0.196
MA0067.1	MA0067.1	0.134
MA0068.1	MA0068.1	0.809
MA0069.1	MA0069.1	0.19
MA0070.1	MA0070.1	0.427
MA0071.1	MA0071.1	0.64
MA0072.1	MA0072.1	0.334
MA0073.1	MA0073.1	0.85
MA0074.1	MA0074.1	0.107
MA0076.1	MA0076.1	1.00789e-6
MA0077.1	MA0077.1	0.444
MA0078.1	MA0078.1	0.963
MA0079.2	MA0079.2	0.0196
MA0080.2	MA0080.2	0.423
MA0081.1	MA0081.1	0.381
MA0083.1	MA0083.1	0.315
MA0084.1	MA0084.1	0.507
MA0087.1	MA0087.1	0.91
MA0088.1	MA0088.1	0.453
MA0090.1	MA0090.1	0.436
MA0091.1	MA0091.1	0.872
MA0092.1	MA0092.1	0.491
MA0093.1	MA0093.1	0.711
MA0099.2	MA0099.2	0.00509
MA0100.1	MA0100.1	0.306
MA0101.1	MA0101.1	0.873
MA0102.2	MA0102.2	0.242
MA0103.1	MA0103.1	0.412
MA0104.2	MA0104.2	0.598
MA0105.1	MA0105.1	0.252
MA0106.1	MA0106.1	0.152
MA0107.1	MA0107.1	0.999
MA0108.2	MA0108.2	0.271
MA0111.1	MA0111.1	0.261
MA0112.2	MA0112.2	0.0959
MA0113.1	MA0113.1	0.657
MA0114.1	MA0114.1	0.103
MA0115.1	MA0115.1	0.0921
MA0116.1	MA0116.1	0.0867
MA0117.1	MA0117.1	0.448
MA0119.1	MA0119.1	0.271
MA0122.1	MA0122.1	0.724
MA0124.1	MA0124.1	0.759
MA0125.1	MA0125.1	0.943
MA0131.1	MA0131.1	0.0287
MA0135.1	MA0135.1	0.0858
MA0136.1	MA0136.1	0.308
MA0137.2	MA0137.2	0.17
MA0138.2	MA0138.2	0.31
MA0139.1	MA0139.1	0.373
MA0140.1	MA0140.1	7.16934e-4
MA0141.1	MA0141.1	0.385
MA0142.1	MA0142.1	0.96
MA0143.1	MA0143.1	0.8
MA0144.1	MA0144.1	0.269
MA0145.1	MA0145.1	0.0527
MA0146.1	MA0146.1	0.0473
MA0147.1	MA0147.1	0.621
MA0148.1	MA0148.1	0.041
MA0149.1	MA0149.1	0.398
MA0150.1	MA0150.1	0.971
MA0152.1	MA0152.1	0.166
MA0153.1	MA0153.1	3.96012e-5
MA0154.1	MA0154.1	0.0325
MA0155.1	MA0155.1	0.0555
MA0156.1	MA0156.1	1.4371e-4
MA0157.1	MA0157.1	0.507
MA0159.1	MA0159.1	0.523
MA0160.1	MA0160.1	0.429
MA0162.1	MA0162.1	0.303
MA0163.1	MA0163.1	0.0154
MA0164.1	MA0164.1	0.926
MA0258.1	MA0258.1	0.234
MA0259.1	MA0259.1	0.141

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: CNhs12629

Novel motif	Logo	P-value
1	1	0.905
10	10	0.927
100	100	0.671
101	101	0.583
102	102	0.778
103	103	0.623
104	104	0.765
105	105	0.779
106	106	0.0109
107	107	0.124
108	108	0.128
109	109	0.137
11	11	0.24
110	110	0.719
111	111	0.983
112	112	0.668
113	113	0.759
114	114	0.446
115	115	0.558
116	116	0.00814
117	117	0.338
118	118	0.78
119	119	0.777
12	12	0.784
120	120	0.314
121	121	0.183
122	122	0.698
123	123	0.837
124	124	0.704
125	125	0.549
126	126	0.427
127	127	0.726
128	128	0.04
129	129	0.704
13	13	0.414
130	130	0.887
131	131	0.692
132	132	0.111
133	133	0.64
134	134	0.714
135	135	0.0673
136	136	0.375
137	137	0.511
138	138	0.944
139	139	0.705
14	14	0.324
140	140	0.395
141	141	0.775
142	142	0.026
143	143	0.17
144	144	0.911
145	145	0.89
146	146	0.315
147	147	0.874
148	148	0.283
149	149	0.0281
15	15	0.789
150	150	0.242
151	151	0.21
152	152	0.0414
153	153	0.51
154	154	0.164
155	155	0.576
156	156	0.0537
157	157	0.321
158	158	0.0364
159	159	0.206
160	160	0.656
161	161	0.497
162	162	0.455
163	163	0.288
164	164	0.0354
165	165	0.669
166	166	0.856
167	167	0.0182
168	168	0.907
169	169	0.0881
17	17	0.279
18	18	0.259
19	19	0.188
2	2	0.0538
20	20	0.562
21	21	0.265
22	22	0.0895
23	23	0.0111
24	24	0.515
25	25	0.402
26	26	0.43
27	27	0.329
28	28	0.592
29	29	0.791
3	3	0.43
30	30	0.109
31	31	0.259
32	32	0.00286
33	33	0.881
34	34	0.0461
35	35	0.792
36	36	0.831
37	37	0.348
38	38	0.347
39	39	0.425
4	4	0.355
40	40	0.497
41	41	0.967
42	42	0.608
43	43	0.128
44	44	0.142
45	45	0.222
46	46	0.698
47	47	0.515
48	48	0.563
49	49	0.458
5	5	0.403
50	50	0.158
51	51	0.942
52	52	0.0995
53	53	0.542
54	54	0.948
55	55	0.184
56	56	0.162
57	57	0.988
58	58	0.629
59	59	0.00331
6	6	0.825
60	60	0.158
61	61	0.757
62	62	0.902
63	63	0.0968
64	64	0.336
65	65	0.0274
66	66	0.912
67	67	0.257
68	68	0.258
69	69	0.0243
7	7	0.321
70	70	0.198
71	71	0.44
72	72	0.72
73	73	0.0966
74	74	0.549
75	75	0.844
76	76	0.241
77	77	0.00658
78	78	0.283
79	79	0.949
8	8	0.362
80	80	0.64
81	81	0.0563
82	82	0.743
83	83	0.529
84	84	0.519
85	85	0.133
86	86	0.921
87	87	0.0276
88	88	0.113
89	89	0.387
9	9	0.437
90	90	0.193
91	91	0.224
92	92	0.345
93	93	0.182
94	94	0.106
95	95	0.187
96	96	0.201
97	97	0.679
98	98	0.0917
99	99	0.27

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: CNhs12629

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000113 mouse microglial 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)
0000003 (native cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000766 (myeloid leukocyte)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000878 (central nervous system macrophage)
0000219 (motile cell)
0000325 (stuff accumulating cell)
0000473 (defensive cell)
0000234 (phagocyte)
0000125 (glial cell)
0000738 (leukocyte)
0000255 (eukaryotic cell)
0000235 (macrophage)
0000864 (tissue-resident macrophage)
0000129 (microglial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000113 (mouse microglial 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:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002371,UBERON:0001474,UBERON:0002384,UBERON:0000926,UBERON:0000479,UBERON:0000073,UBERON:0004121,UBERON:0000062,UBERON:0004765,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000467,UBERON:0001062,UBERON:0005291,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0001016,UBERON:0002204,UBERON:0001434,UBERON:0000924,UBERON:0002390,UBERON:0005743,UBERON:0002193,UBERON:0002405,UBERON:0003081,UBERON:0006601,UBERON:0006603,UBERON:0003061
+|DRA_sample_Accession=CAGE@SAMD00005195
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000333,CL:0000055,CL:0000144,CL:0000723,CL:0000048,CL:0000988,CL:0000839,CL:0000548,CL:0002194,CL:0000034,CL:0002032,CL:0000763,CL:0000012,CL:0002321,CL:0002320,CL:0000063,CL:0002371,CL:0000864,CL:0000766,CL:0002319,CL:0000221,CL:0000095,CL:0000243,CL:0000878,CL:0000219,CL:0000220,CL:0000123,CL:0000125,CL:0000004,CL:0000134,CL:0000030,CL:0000738,CL:0002087,CL:0000255,CL:0002031,CL:0000576,CL:0000235,CL:0000037,CL:0000566,CL:0000049,CL:0000557,CL:0000129,CL:0002453,CL:0000837,CL:0000133,CL:0002009,CL:0000339,CL:0000040,CL:0000559
+|accession_numbers=CAGE;DRX008828;DRR009700;DRZ001125;DRZ002510;DRZ012475;DRZ013860
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000479,UBERON:0004121,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001017,UBERON:0001016
+|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0000763,CL:0002371,CL:0000766,CL:0002319,CL:0000095,CL:0000243,CL:0000878,CL:0000219,CL:0000325,CL:0000473,CL:0000234,CL:0000125,CL:0000738,CL:0000255,CL:0000235,CL:0000864,CL:0000129
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000113
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.93!975.20!Olig1;;chr16:91225808..91225824,+!p1@Olig2!2.30!197.74!Olig2;;chr11:116196664..116196679,-!p1@Foxj1!2.26!275.03!Foxj1;;chr5:138199361..138199441,+!p2@Tsc22d4!2.10!228.30!Tsc22d4;;chr13:99124189..99124205,+!p1@Foxd1!1.93!125.23!Foxd1;;chr16:91270091..91270143,+!p2@Olig1!1.83!66.81!Olig1;;chr3:34548909..34548927,+!p1@Sox2!1.74!88.98!Sox2;;chr2:90936901..90936945,+!p1@Sfpi1!1.59!188.75!Sfpi1;;chr17:25707623..25707639,-!p1@Sox8!1.56!145.91!Sox8;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.55!42.84!Pou3f3;;chr14:122874619..122874634,+!p1@Zic2!1.53!32.96!Zic2;;chr3:34548946..34548972,+!p2@Sox2!1.39!26.07!Sox2;;chr15:78994907..78994926,-!p1@Sox10!1.35!53.33!Sox10;;chrX:58146612..58146615,-!p1@Sox3!1.35!21.27!Sox3;;chr9:91260616..91260653,-!p2@Zic1!1.34!20.97!Zic1;;chr7:25292141..25292158,+!p2@Zfp428!1.32!67.71!Zfp428;;chr4:99322820..99322845,+!p1@Foxd3!1.30!23.97!Foxd3;;chr9:91260594..91260612,-!p1@Zic1!1.30!19.17!Zic1;;chr12:86814833..86814846,+!p1@Fos!1.29!414.65!Fos;;chr13:31898767..31898785,+!p4@Foxc1!1.29!22.47!Foxc1;;chr5:38215819..38215823,-!p1@Msx1!1.27!45.24!Msx1;;chr1:193007123..193007139,-!p1@Atf3!1.25!91.68!Atf3;;chr10:86956396..86956411,-!p1@Ascl1!1.25!26.07!Ascl1;;chr12:54349410..54349461,+!p1@Npas3!1.25!20.07!Npas3;;chr12:34642510..34642530,+!p1@Twist1!1.24!51.83!Twist1;;chr14:118636214..118636235,-!p1@Sox21!1.24!19.77!Sox21;;chr13:31898496..31898519,+!p3@Foxc1!1.23!25.77!Foxc1;;chr4:107353376..107353452,-!p3@Dmrtb1!1.23!16.18!Dmrtb1;;chr8:87225329..87225396,+!p1@Lyl1!1.22!58.12!Lyl1;;chr6:29476690..29476724,+!p1@Irf5!1.20!67.41!Irf5;;chr13:31898637..31898653,+!p2@Foxc1!1.20!26.66!Foxc1;;chr4:135699731..135699747,+!p1@Id3!1.18!1564.81!Id3;;chr11:5761979..5761992,+!p2@Aebp1!1.18!28.46!Aebp1;;chr2:90936947..90936977,+!p2@Sfpi1!1.18!27.86!Sfpi1;;chr16:15887371..15887385,+!p1@Cebpd!1.17!458.39!Cebpd;;chr2:38206744..38206766,+!p1@Lhx2!1.17!16.78!Lhx2;;chr2:90936978..90937023,+!p3@Sfpi1!1.16!25.47!Sfpi1;;chr14:118636238..118636257,-!p2@Sox21!1.14!12.88!Sox21;;chr2:160192793..160192809,-!p1@Mafb!1.11!180.36!Mafb;;chr11:5761889..5761969,+!p1@Aebp1!1.10!484.45!Aebp1;;chrX:90531838..90531861,+!p1@Arx!1.10!14.68!Arx;;chr3:34549096..34549111,+!p3@Sox2!1.10!11.68!Sox2;;chr6:145814003..145814056,-!p1@Bhlhe41!1.08!32.36!Bhlhe41;;chr13:31898729..31898761,+!p1@Foxc1!1.08!27.26!Foxc1;;chr8:123640063..123640077,+!p1@Foxc2!1.08!20.07!Foxc2;;chr5:148000254..148000260,+!p1@Gsx1!1.08!11.09!Gsx1;;chr10:84218895..84218909,+!p1@Rfx4!1.08!11.09!Rfx4;;chr6:145813905..145813932,-!p2@Bhlhe41!1.07!20.67!Bhlhe41;;chr7:52960700..52960719,+!p2@Dbp!1.07!13.18!Dbp;;chr7:35904304..35904320,+!p1@Cebpa!1.06!213.32!Cebpa;;chr2:30700881..30700916,+!p1@Prrx2!1.06!20.07!Prrx2;;chrX:108009761..108009788,+!p1@Pou3f4!1.06!10.49!Pou3f4;;chr5:28492230..28492257,+!p1@En2!1.06!10.49!En2;;chrX:7341077..7341091,+!p5@Tfe3!1.03!16.48!Tfe3;;chr2:30700857..30700873,+!p3@Prrx2!1.03!13.48!Prrx2;;chr17:86087592..86087615,-!p1@Six2!1.02!9.59!Six2;;chr13:48356475..48356492,+!p1@Id4!1.01!203.73!Id4;;chr8:12395603..12395621,+!p1@Sox1!1.01!9.29!Sox1;;chr15:103170516..103170531,-!p2@Zfp385a!1.00!21.57!Zfp385a;;chr10:84218800..84218829,+!p2@Rfx4!1.00!8.99!Rfx4;;chr7:52960555..52960662,+!p1@Dbp!0.99!75.50!Dbp;;chr8:123260252..123260264,+!p1@Irf8!0.98!62.02!Irf8;;chr9:106356278..106356292,+!p3@Pcbp4!0.98!14.98!Pcbp4;;chr16:92697560..92697592,-!p2@Runx1!0.96!52.43!Runx1;;chr12:74147689..74147711,-!p1@Six1!0.96!18.28!Six1;;chr13:53568104..53568156,-!p1@Msx2!0.96!12.28!Msx2;;chr2:173044380..173044432,-!p1@Zbp1!0.95!19.17!Zbp1;;chr10:67000609..67000625,+!p1@Egr2!0.95!18.58!Egr2;;chr2:127347067..127347093,-!p1@Kcnip3!0.95!13.48!Kcnip3;;chr18:35020854..35020869,+!p1@Egr1!0.94!307.99!Egr1;;chrX:7339938..7339963,+!p1@Tfe3!0.94!40.45!Tfe3;;chr19:5447886..5447905,+!p1@Fosl1!0.94!7.79!Fosl1;;chr13:99124236..99124243,+!p2@Foxd1!0.94!7.79!Foxd1;;chr14:122874593..122874610,+!p2@Zic2!0.93!7.49!Zic2;;chr11:112643496..112643562,+!p1@Sox9!0.92!281.62!Sox9;;chr5:77524250..77524300,-!p1@Hopx!0.92!153.69!Hopx;;chr8:87502608..87502623,-!p1@Junb!0.91!121.34!Junb;;chr7:52960663..52960677,+!p6@Dbp!0.91!7.19!Dbp;;chr15:103170533..103170556,-!p1@Zfp385a!0.90!26.96!Zfp385a;;chr7:87170879..87170914,+!p2@Zfp710!0.89!16.18!Zfp710;;chr7:146768691..146768707,-!p1@Nkx6-2!0.88!6.59!Nkx6-2;;chr16:91269972..91269978,+!p3@Olig1!0.88!6.59!Olig1;;chr16:91225654..91225671,+!p2@Olig2!0.88!6.59!Olig2;;chr11:60023912..60023930,-!p1@Srebf1!0.87!163.58!Srebf1;;chr17:27693887..27693908,+!p2@Hmga1-rs1,p2@Hmga1!0.86!47.64!Hmga1;;chr9:106356243..106356264,+!p2@Pcbp4!0.86!28.46!Pcbp4;;chr2:90922554..90922575,+!p4@Sfpi1!0.86!11.68!Sfpi1;;chr4:107353455..107353476,-!p8@Dmrtb1!0.86!6.29!Dmrtb1;;chr3:34549144..34549155,+!p5@Sox2!0.86!6.29!Sox2;;chr4:107353346..107353375,-!p5@Dmrtb1!0.86!6.29!Dmrtb1;;chr6:72185232..72185272,-!p1@Atoh8!0.85!18.28!Atoh8;;chr13:78339476..78339515,-!p1@Nr2f1!0.85!9.59!Nr2f1;;chr3:8666963..8666978,-!p1@Hey1!0.84!40.45!Hey1;;chr3:8666997..8667012,-!p2@Hey1!0.84!14.38!Hey1;;chr2:147012125..147012149,-!p1@Nkx2-2!0.84!5.99!Nkx2-2;;chr4:154010409..154010466,-!p2@Prdm16!0.83!14.08!Prdm16;;chr7:122968213..122968266,-!p4@Sox6!0.83!6.89!Sox6;;chr13:40829137..40829205,-!p1@Tfap2a!0.83!6.59!Tfap2a;;chr7:108966820..108966835,+!p1@Phox2a!0.83!5.69!Phox2a;;chr11:98636531..98636559,-!p1@Nr1d1!0.82!34.45!Nr1d1;;chr3:99057269..99057306,+!p1@Tbx15!0.82!6.89!Tbx15;;chr7:52071956..52071978,-!p1@Atf5!0.81!192.64!Atf5;;chr12:9581284..9581303,+!p2@Osr1!0.81!11.09!Osr1;;chr7:25917492..25917512,-!p1@Pou2f2!0.81!9.59!Pou2f2;;chr8:87238155..87238187,-!p13@Nfix!0.81!5.39!Nfix;;chr11:21901608..21901634,-!p1@Otx1!0.81!5.39!Otx1;;chr7:26067619..26067702,+!p2@Cic!0.80!32.66!Cic;;chr14:52634234..52634281,-!p3@Zfp219!0.80!15.58!Zfp219;;chr6:72185210..72185228,-!p3@Atoh8!0.80!9.29!Atoh8;;chr3:32264530..32264544,-!p2@Zmat3!0.80!8.69!Zmat3;;chr2:90936886..90936898,+!p5@Sfpi1!0.79!6.29!Sfpi1;;chr12:9581262..9581282,+!p1@Osr1!0.78!65.91!Osr1;;chr19:28754692..28754757,-!p1@Glis3!0.78!22.47!Glis3;;chr17:56970339..56970428,-!p1@Rfx2!0.78!17.08!Rfx2;;chr7:25292160..25292213,+!p3@Zfp428!0.78!13.48!Zfp428;;chr3:34548845..34548856,+!p4@Sox2!0.78!5.09!Sox2;;chr14:122874718..122874729,+!p3@Zic2!0.78!5.09!Zic2;;chr12:34642682..34642753,+!p2@Twist1!0.77!13.78!Twist1;;chr5:77524231..77524245,-!p3@Hopx!0.77!12.88!Hopx;;chr8:87297280..87297326,-!p2@Nfix!0.77!12.28!Nfix;;chr2:167514456..167514473,+!p1@Cebpb!0.76!233.39!Cebpb;;chr2:152561980..152561997,+!p1@Id1!0.76!153.10!Id1;;chr9:106356211..106356242,+!p1@Pcbp4!0.76!103.06!Pcbp4;;chr17:34784132..34784161,+!p1@Atf6b!0.76!29.66!Atf6b;;chr15:95485240..95485257,-!p1@Dbx2!0.76!4.79!Dbx2;;chr3:32264565..32264613,-!p1@Zmat3!0.75!56.03!Zmat3;;chr11:11586218..11586285,+!p1@Ikzf1!0.75!16.18!Ikzf1;;chr1:186556410..186556424,-!p1@Hlx!0.75!15.58!Hlx;;chr6:72185553..72185612,-!p2@Atoh8!0.74!9.29!Atoh8;;chr2:71384802..71384815,-!p1@Dlx2!0.74!5.69!Dlx2;;chr2:147019977..147019985,-!p2@Nkx2-2!0.74!4.49!Nkx2-2;;chr14:34791937..34791977,-!p1@Zfp488!0.74!4.49!Zfp488;;chr8:28087609..28087634,+!p1@Zfp703!0.73!111.45!Zfp703;;chr7:25292076..25292114,+!p4@Zfp428!0.73!12.88!Zfp428;;chr12:9581317..9581333,+!p3@Osr1!0.73!6.89!Osr1;;chr13:72101178..72101203,-!p1@Irx1!0.72!6.89!Irx1;;chr19:5423800..5423821,-!p5@Drap1!0.72!6.59!Drap1;;chr3:107398056..107398082,+!p1@Alx3!0.72!4.19!Alx3;;chr5:138199339..138199346,+!p18@Tsc22d4!0.72!4.19!Tsc22d4;;chr14:118635860..118635885,-!p3@Sox21!0.72!4.19!Sox21;;chr2:30700788..30700824,+!p2@Prrx2!0.71!6.59!Prrx2;;chr7:52960730..52960762,+!p3@Dbp!0.71!5.39!Dbp;;chr4:154335024..154335039,+!p1@Hes5!0.71!5.09!Hes5;;chr8:87225670..87225697,+!p2@Lyl1!0.70!12.88!Lyl1;;chr8:87297878..87297935,-!p3@Nfix!0.70!9.59!Nfix;;chr16:92697354..92697362,-!p3@Runx1!0.70!6.59!Runx1;;chr7:20408047..20408125,-!p1@Bcl3!0.69!50.63!Bcl3;;chr9:106356265..106356276,+!p4@Pcbp4!0.69!6.89!Pcbp4;;chr13:31898529..31898542,+!p5@Foxc1!0.69!4.79!Foxc1;;chr4:114581497..114581519,-!p2@Foxd2!0.69!3.89!Foxd2;;chr10:42303385..42303401,-!p1@Nr2e1!0.69!3.89!Nr2e1;;chr2:168415815..168415872,-!p1@Nfatc2!0.68!23.37!Nfatc2;;chr17:45692676..45692695,+!p2@Nfkbie!0.68!8.39!Nfkbie;;chr11:120491440..120491474,-!p3@Mafg!0.67!5.69!Mafg;;chr9:87626083..87626108,-!p1@Tbx18!0.66!8.69!Tbx18;;chr2:127347094..127347111,-!p2@Kcnip3!0.66!6.29!Kcnip3;;chr2:173044357..173044377,-!p2@Zbp1!0.66!5.39!Zbp1;;chr1:91827756..91827773,-!p1@Gbx2!0.66!3.60!Gbx2;;chr8:12395892..12395919,+!p4@Sox1!0.66!3.60!Sox1;;chr15:95485210..95485225,-!p2@Dbx2!0.66!3.60!Dbx2;;chr4:109650609..109650653,+!p1@Dmrta2!0.66!3.60!Dmrta2;;chr4:94718879..94718898,-!p1@Jun!0.65!293.61!Jun;;chr19:46379199..46379301,+!p1@Nfkb2!0.65!23.07!Nfkb2;;chr10:80870405..80870428,-!p4@Nfic!0.65!10.49!Nfic;;chr2:90922519..90922544,+!p6@Sfpi1!0.65!3.89!Sfpi1;;chr7:133839456..133839523,+!p1@Bola2!0.63!190.85!Bola2;;chr9:32348943..32349001,-!p1@Fli1!0.63!31.46!Fli1;;chr7:25292331..25292421,+!p1@Zfp428!0.63!27.26!Zfp428;;chr19:55816546..55816556,+!p3@Tcf7l2!0.63!14.38!Tcf7l2;;chr7:20214704..20214800,-!p1@Relb!0.63!12.28!Relb;;chr10:67375368..67375433,-!p1@Zfp365!0.63!6.29!Zfp365;;chr3:8667033..8667046,-!p3@Hey1!0.63!4.79!Hey1;;chr4:154010228..154010244,-!p4@Prdm16!0.63!4.79!Prdm16;;chr18:81183755..81183761,-!p1@Sall3!0.63!3.30!Sall3;;chr2:147012101..147012118,-!p3@Nkx2-2!0.63!3.30!Nkx2-2;;chr9:91263649..91263666,+!p3@Zic4!0.63!3.30!Zic4;;chr8:28087578..28087599,+!p2@Zfp703!0.62!36.25!Zfp703;;chr19:5637528..5637548,+!p2@Rela!0.62!21.87!Rela;;chr2:25562315..25562344,+!p3@Bmyc!0.62!12.28!Bmyc;;chr2:27532479..27532509,+!p3@Rxra!0.62!7.19!Rxra;;chr6:145813964..145813994,-!p3@Bhlhe41!0.62!4.19!Bhlhe41;;chr11:96690797..96690813,-!p1@Nfe2l1!0.61!70.71!Nfe2l1;;chrX:7339829..7339855,+!p3@Tfe3!0.61!9.29!Tfe3;;chrX:7339915..7339935,+!p4@Tfe3!0.61!7.79!Tfe3;;chr11:5761871..5761882,+!p3@Aebp1!0.60!8.99!Aebp1;;chr1:186556375..186556404,-!p3@Hlx!0.60!5.99!Hlx;;chr4:114581524..114581551,-!p1@Foxd2!0.60!4.79!Foxd2;;chr2:90936867..90936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+|ffid_belonging_in_development=CL:0000133,CL:0000049,CL:0000134,CL:0000339,CL:0000221
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000113
 |is_obsolete=
+|library_id=CNhs12629
+|library_id_phase_based=2:CNhs12629
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11718
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11718
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor1.CNhs12629.11718-123C8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor1.CNhs12629.11718-123C8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor1.CNhs12629.11718-123C8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor1.CNhs12629.11718-123C8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor1.CNhs12629.11718-123C8.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Microglia, donor1
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12629,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.78617072020651,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.576636951319453,-0.444613052718544,0,0,0,0,0,-0.0700830760559312,0.157628137726286,-0.0789606644490415,-0.537425644236559,-0.269868638010351,0.531070089863674,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0.0681071401479631,0,0,0,-0.20244242069718,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,0.0649026233549767,0.118534948546826,0,0,0,-0.056627664597195,0.903211260054181,-0.0788315948399074,0,0,0,0,0,0,0.496195012586388,0.432522174889431,0.368104460966856,0,0,0.113809739605487,0.342106802711204,0
 |rna_box=123
 |rna_catalog_number=custom
@@ Line 58: / Line 76: @@
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11718-123C8;search_select_hide=table117:11718-123C8
 }}

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FF:11718-123C8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:16, 4 June 2020

CNhs12629

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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