FF:11716-123C6: Difference between revisions

Latest revision as of 18:16, 4 June 2020

Name:	Mouse Meningeal cells, donor1
Species:	Mouse (Mus musculus)
Library ID:	CNhs12132
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	meninges
dev stage	NA
sex	NA
age	NA
cell type	meningeal 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	RNAM5762
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		SAMD00005064

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12132		CAGE		DRX008823		DRR009695

Accession ID Mm9

Library id		BAM		CTSS
CNhs12132		DRZ001120		DRZ002505

Accession ID Mm10

Library id		BAM		CTSS
CNhs12132		DRZ012470		DRZ013855

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

CNhs12132

0	0
1	0
10	0
100	0
1000	0.0262
1001	-0.0749
1002	0.0145
1003	0.0194
1004	0
1005	0
1006	-0.0223
1007	-0.352
1008	0
1009	0.115
101	-0.387
1010	0
1011	-0.108
1012	0
1013	0.0264
1014	-0.0851
1015	0.337
1016	0.19
1017	0
1018	0
1019	0
102	0
1020	0.481
1021	0.127
1022	-0.124
1023	0
1024	-0.18
1025	-0.0611
1026	0
1027	0
1028	0
1029	-0.176
103	0.342
1030	0
1031	0.993
1032	0.0411
1033	0.0611
1034	0
1035	0
1036	-0.00647
1037	0
1038	-0.0736
1039	-0.0747
104	0
1040	0.545
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: CNhs12132

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0993
MA0003.1	MA0003.1	0.307
MA0004.1	MA0004.1	0.0965
MA0006.1	MA0006.1	0.639
MA0007.1	MA0007.1	0.206
MA0009.1	MA0009.1	0.471
MA0014.1	MA0014.1	0.326
MA0017.1	MA0017.1	0.0838
MA0018.2	MA0018.2	0.128
MA0019.1	MA0019.1	0.737
MA0024.1	MA0024.1	5.32971e-4
MA0025.1	MA0025.1	0.961
MA0027.1	MA0027.1	0.497
MA0028.1	MA0028.1	0.545
MA0029.1	MA0029.1	0.869
MA0030.1	MA0030.1	0.288
MA0031.1	MA0031.1	0.596
MA0035.2	MA0035.2	0.101
MA0038.1	MA0038.1	0.0362
MA0039.2	MA0039.2	0.0884
MA0040.1	MA0040.1	0.627
MA0041.1	MA0041.1	0.241
MA0042.1	MA0042.1	0.701
MA0043.1	MA0043.1	0.34
MA0046.1	MA0046.1	6.51843e-6
MA0047.2	MA0047.2	0.226
MA0048.1	MA0048.1	0.126
MA0050.1	MA0050.1	0.0907
MA0051.1	MA0051.1	0.101
MA0052.1	MA0052.1	0.0681
MA0055.1	MA0055.1	8.40847e-4
MA0057.1	MA0057.1	0.435
MA0058.1	MA0058.1	0.0489
MA0059.1	MA0059.1	0.177
MA0060.1	MA0060.1	0.16
MA0061.1	MA0061.1	0.338
MA0062.2	MA0062.2	0.0929
MA0065.2	MA0065.2	0.912
MA0066.1	MA0066.1	0.274
MA0067.1	MA0067.1	0.539
MA0068.1	MA0068.1	0.788
MA0069.1	MA0069.1	0.672
MA0070.1	MA0070.1	0.676
MA0071.1	MA0071.1	0.757
MA0072.1	MA0072.1	0.685
MA0073.1	MA0073.1	0.653
MA0074.1	MA0074.1	0.0703
MA0076.1	MA0076.1	0.117
MA0077.1	MA0077.1	0.0753
MA0078.1	MA0078.1	0.085
MA0079.2	MA0079.2	0.123
MA0080.2	MA0080.2	0.00622
MA0081.1	MA0081.1	0.275
MA0083.1	MA0083.1	2.16925e-8
MA0084.1	MA0084.1	0.806
MA0087.1	MA0087.1	0.933
MA0088.1	MA0088.1	0.664
MA0090.1	MA0090.1	3.79189e-5
MA0091.1	MA0091.1	0.815
MA0092.1	MA0092.1	0.0461
MA0093.1	MA0093.1	0.141
MA0099.2	MA0099.2	1.26425e-8
MA0100.1	MA0100.1	0.588
MA0101.1	MA0101.1	0.694
MA0102.2	MA0102.2	0.135
MA0103.1	MA0103.1	0.00127
MA0104.2	MA0104.2	0.471
MA0105.1	MA0105.1	0.419
MA0106.1	MA0106.1	2.24174e-5
MA0107.1	MA0107.1	0.9
MA0108.2	MA0108.2	0.206
MA0111.1	MA0111.1	0.719
MA0112.2	MA0112.2	0.0632
MA0113.1	MA0113.1	0.532
MA0114.1	MA0114.1	0.366
MA0115.1	MA0115.1	0.265
MA0116.1	MA0116.1	0.16
MA0117.1	MA0117.1	0.377
MA0119.1	MA0119.1	0.243
MA0122.1	MA0122.1	0.745
MA0124.1	MA0124.1	0.233
MA0125.1	MA0125.1	0.74
MA0131.1	MA0131.1	0.386
MA0135.1	MA0135.1	0.219
MA0136.1	MA0136.1	0.0435
MA0137.2	MA0137.2	0.425
MA0138.2	MA0138.2	0.0115
MA0139.1	MA0139.1	0.771
MA0140.1	MA0140.1	4.85286e-4
MA0141.1	MA0141.1	0.408
MA0142.1	MA0142.1	0.557
MA0143.1	MA0143.1	0.411
MA0144.1	MA0144.1	0.728
MA0145.1	MA0145.1	0.0352
MA0146.1	MA0146.1	0.00837
MA0147.1	MA0147.1	0.409
MA0148.1	MA0148.1	0.155
MA0149.1	MA0149.1	0.313
MA0150.1	MA0150.1	0.663
MA0152.1	MA0152.1	0.298
MA0153.1	MA0153.1	7.90682e-4
MA0154.1	MA0154.1	0.199
MA0155.1	MA0155.1	0.343
MA0156.1	MA0156.1	1.66572e-4
MA0157.1	MA0157.1	0.498
MA0159.1	MA0159.1	0.771
MA0160.1	MA0160.1	0.796
MA0162.1	MA0162.1	0.222
MA0163.1	MA0163.1	0.0402
MA0164.1	MA0164.1	0.86
MA0258.1	MA0258.1	0.175
MA0259.1	MA0259.1	0.698

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: CNhs12132

Novel motif	Logo	P-value
1	1	0.922
10	10	0.797
100	100	0.764
101	101	0.845
102	102	0.159
103	103	0.415
104	104	0.656
105	105	0.298
106	106	0.0543
107	107	0.923
108	108	0.358
109	109	0.00195
11	11	0.0152
110	110	0.132
111	111	0.473
112	112	0.971
113	113	0.381
114	114	0.209
115	115	0.732
116	116	0.0146
117	117	0.332
118	118	0.941
119	119	0.402
12	12	0.774
120	120	0.602
121	121	0.275
122	122	0.269
123	123	0.57
124	124	0.0792
125	125	0.282
126	126	0.866
127	127	0.169
128	128	0.491
129	129	0.873
13	13	0.492
130	130	0.363
131	131	0.559
132	132	0.479
133	133	0.535
134	134	0.379
135	135	0.407
136	136	0.112
137	137	0.312
138	138	0.724
139	139	0.435
14	14	0.453
140	140	0.789
141	141	0.684
142	142	0.353
143	143	0.0448
144	144	0.375
145	145	0.105
146	146	0.876
147	147	0.537
148	148	0.491
149	149	0.112
15	15	0.795
150	150	0.227
151	151	0.961
152	152	0.0243
153	153	0.255
154	154	0.253
155	155	0.382
156	156	0.0201
157	157	0.295
158	158	0.222
159	159	0.199
160	160	0.935
161	161	0.57
162	162	0.475
163	163	0.256
164	164	0.836
165	165	0.719
166	166	0.833
167	167	0.0195
168	168	0.942
169	169	0.0842
17	17	0.0613
18	18	0.371
19	19	0.168
2	2	0.261
20	20	0.508
21	21	0.0851
22	22	0.0503
23	23	0.128
24	24	0.151
25	25	0.115
26	26	0.174
27	27	0.755
28	28	0.314
29	29	0.405
3	3	0.268
30	30	0.587
31	31	0.851
32	32	0.0716
33	33	0.831
34	34	0.217
35	35	0.124
36	36	0.507
37	37	0.0577
38	38	0.206
39	39	0.497
4	4	0.25
40	40	0.0478
41	41	0.329
42	42	0.274
43	43	0.25
44	44	0.197
45	45	0.495
46	46	0.552
47	47	0.189
48	48	0.495
49	49	0.561
5	5	0.411
50	50	0.0532
51	51	0.504
52	52	0.242
53	53	0.949
54	54	0.443
55	55	0.501
56	56	0.391
57	57	0.509
58	58	0.27
59	59	0.0121
6	6	0.401
60	60	0.299
61	61	0.758
62	62	0.821
63	63	0.189
64	64	0.301
65	65	0.0271
66	66	0.364
67	67	0.596
68	68	0.737
69	69	0.0839
7	7	0.443
70	70	0.0918
71	71	0.362
72	72	0.833
73	73	0.00353
74	74	0.501
75	75	0.2
76	76	0.672
77	77	0.00887
78	78	0.684
79	79	0.907
8	8	0.269
80	80	0.259
81	81	0.387
82	82	0.973
83	83	0.542
84	84	0.52
85	85	0.0473
86	86	0.86
87	87	0.00461
88	88	0.424
89	89	0.816
9	9	0.972
90	90	0.236
91	91	0.344
92	92	0.46
93	93	0.823
94	94	0.512
95	95	0.00574
96	96	0.503
97	97	0.869
98	98	0.252
99	99	0.986

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: CNhs12132

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000111 mouse leptomeningeal 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)
0000548 (animal cell)
0000151 (secretory cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000499 (stromal cell)
0000327 (extracellular matrix secreting cell)
0000255 (eukaryotic cell)
0000708 (leptomeningeal cell)

UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0000119 (cell layer)
0003210 (blood-cerebrospinal fluid barrier)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000111 (mouse leptomeningeal 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:0000134 (mesenchymal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008713
+|DRA_sample_Accession=CAGE@SAMD00005064
+|accession_numbers=CAGE;DRX008823;DRR009695;DRZ001120;DRZ002505;DRZ012470;DRZ013855
 |ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062,UBERON:0000119,UBERON:0003210
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000151,CL:0002320,CL:0002371,CL:0000499,CL:0000327,CL:0000255,CL:0000708
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000111
 |is_obsolete=
-|library_ids=CNhs12132
+|library_id=CNhs12132
+|library_id_phase_based=2:CNhs12132
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11716
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11716
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Meningeal cells, donor1
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12132,LSID839,release011,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.742007379290395,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0.126730149241647,0,0,0,0,0,0,0.29838605578396,-0.558422792324031,0,0,0,0,0,-0.209322725495826,0,0.0194164925409261,-0.85748121723618,-0.269868638010351,0.22471147363102,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0,-0.0530480122014902,-0.243225778194271,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,-0.0509130794431689,0,0,0,-0.08197012070238,-0.005430402315432,0.68958852586577,-0.0788315948399074,0,0,0,0,0,0,0.396105485369212,0.155142398655853,0.0149282119531575,0,0,0.126730149241647,0.226650023692595,0
@@ Line 85: / Line 97: @@
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 |xref=
-}} {{DRAAccessionNumbers
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11716-123C6;search_select_hide=table117:11716-123C6
-|DRA_sample_Accession=CAGE@DRS008713
-|accession_numbers=DRX008823;DRR009695;DRZ001120;DRZ002505;CAGE
-|library_id=CNhs12132
 }}

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From FANTOM5_SSTAR

Latest revision as of 18:16, 4 June 2020

CNhs12132

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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