FF:12127-128D3: Difference between revisions

Latest revision as of 18:31, 4 June 2020

Name:	stem cell (cKit+ Sca1- lineage-) KSL, biol_rep3
Species:	Mouse (Mus musculus)
Library ID:	CNhs12536
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/8J
tissue	bone marrow
dev stage	NA
sex	male
age	9-10weeks
cell type	stem cell (cKit+ Sca1- lineage-)
cell line	NA
company	NA
collaboration	Kitamura/Nakahara
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	rep3
catalog number	NA
sample type	total RNA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005934

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12536		CAGE		DRX008786		DRR009658

Accession ID Mm9

Library id		BAM		CTSS
CNhs12536		DRZ001083		DRZ002468

Accession ID Mm10

Library id		BAM		CTSS
CNhs12536		DRZ012433		DRZ013818

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

CNhs12536

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0749
1002	-0.116
1003	-0.155
1004	0
1005	0.151
1006	-0.13
1007	-0.16
1008	0
1009	-0.094
101	0.222
1010	0
1011	0.0431
1012	0
1013	-0.118
1014	-0.0874
1015	-0.00896
1016	-0.332
1017	0
1018	0.0318
1019	0
102	0.106
1020	0.0562
1021	0
1022	-0.0428
1023	0.715
1024	1.013
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.0709
103	-0.0887
1030	0
1031	-0.855
1032	-0.184
1033	0.151
1034	0
1035	0
1036	0.376
1037	0
1038	-0.221
1039	-0.0727
104	0
1040	-0.121
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: CNhs12536

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	3.563e-7
MA0003.1	MA0003.1	0.776
MA0004.1	MA0004.1	0.324
MA0006.1	MA0006.1	0.794
MA0007.1	MA0007.1	0.942
MA0009.1	MA0009.1	0.306
MA0014.1	MA0014.1	0.794
MA0017.1	MA0017.1	0.203
MA0018.2	MA0018.2	2.2323e-11
MA0019.1	MA0019.1	0.6
MA0024.1	MA0024.1	0.00103
MA0025.1	MA0025.1	5.14151e-4
MA0027.1	MA0027.1	0.0217
MA0028.1	MA0028.1	8.72568e-8
MA0029.1	MA0029.1	0.568
MA0030.1	MA0030.1	0.265
MA0031.1	MA0031.1	0.00274
MA0035.2	MA0035.2	0.969
MA0038.1	MA0038.1	0.0169
MA0039.2	MA0039.2	0.123
MA0040.1	MA0040.1	0.0229
MA0041.1	MA0041.1	0.73
MA0042.1	MA0042.1	0.565
MA0043.1	MA0043.1	1.02011e-7
MA0046.1	MA0046.1	7.67912e-16
MA0047.2	MA0047.2	0.521
MA0048.1	MA0048.1	0.0272
MA0050.1	MA0050.1	1.13833e-15
MA0051.1	MA0051.1	2.05586e-9
MA0052.1	MA0052.1	0.803
MA0055.1	MA0055.1	0.0196
MA0057.1	MA0057.1	0.787
MA0058.1	MA0058.1	0.212
MA0059.1	MA0059.1	0.147
MA0060.1	MA0060.1	0.323
MA0061.1	MA0061.1	1.31364e-12
MA0062.2	MA0062.2	2.23329e-21
MA0065.2	MA0065.2	0.874
MA0066.1	MA0066.1	0.229
MA0067.1	MA0067.1	9.07477e-6
MA0068.1	MA0068.1	0.0174
MA0069.1	MA0069.1	0.687
MA0070.1	MA0070.1	0.65
MA0071.1	MA0071.1	0.857
MA0072.1	MA0072.1	0.702
MA0073.1	MA0073.1	0.683
MA0074.1	MA0074.1	0.764
MA0076.1	MA0076.1	7.95089e-8
MA0077.1	MA0077.1	0.228
MA0078.1	MA0078.1	0.884
MA0079.2	MA0079.2	0.771
MA0080.2	MA0080.2	2.70597e-14
MA0081.1	MA0081.1	3.28249e-5
MA0083.1	MA0083.1	0.283
MA0084.1	MA0084.1	0.0656
MA0087.1	MA0087.1	0.672
MA0088.1	MA0088.1	0.435
MA0090.1	MA0090.1	0.00539
MA0091.1	MA0091.1	0.228
MA0092.1	MA0092.1	0.204
MA0093.1	MA0093.1	0.268
MA0099.2	MA0099.2	2.41486e-21
MA0100.1	MA0100.1	0.00471
MA0101.1	MA0101.1	3.82229e-17
MA0102.2	MA0102.2	0.014
MA0103.1	MA0103.1	0.205
MA0104.2	MA0104.2	0.156
MA0105.1	MA0105.1	1.07413e-5
MA0106.1	MA0106.1	0.68
MA0107.1	MA0107.1	1.27482e-18
MA0108.2	MA0108.2	0.343
MA0111.1	MA0111.1	0.948
MA0112.2	MA0112.2	0.924
MA0113.1	MA0113.1	0.76
MA0114.1	MA0114.1	0.00776
MA0115.1	MA0115.1	0.917
MA0116.1	MA0116.1	0.0755
MA0117.1	MA0117.1	0.00802
MA0119.1	MA0119.1	0.0833
MA0122.1	MA0122.1	0.103
MA0124.1	MA0124.1	0.928
MA0125.1	MA0125.1	0.0723
MA0131.1	MA0131.1	0.103
MA0135.1	MA0135.1	0.589
MA0136.1	MA0136.1	6.66287e-30
MA0137.2	MA0137.2	0.00891
MA0138.2	MA0138.2	2.33516e-5
MA0139.1	MA0139.1	0.911
MA0140.1	MA0140.1	0.848
MA0141.1	MA0141.1	0.135
MA0142.1	MA0142.1	0.783
MA0143.1	MA0143.1	0.038
MA0144.1	MA0144.1	0.0685
MA0145.1	MA0145.1	0.772
MA0146.1	MA0146.1	0.0565
MA0147.1	MA0147.1	0.145
MA0148.1	MA0148.1	0.963
MA0149.1	MA0149.1	0.344
MA0150.1	MA0150.1	3.58633e-6
MA0152.1	MA0152.1	0.598
MA0153.1	MA0153.1	5.20765e-6
MA0154.1	MA0154.1	0.936
MA0155.1	MA0155.1	0.388
MA0156.1	MA0156.1	5.59777e-27
MA0157.1	MA0157.1	0.0177
MA0159.1	MA0159.1	0.364
MA0160.1	MA0160.1	0.864
MA0162.1	MA0162.1	0.61
MA0163.1	MA0163.1	0.00462
MA0164.1	MA0164.1	0.663
MA0258.1	MA0258.1	0.338
MA0259.1	MA0259.1	0.385

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: CNhs12536

Novel motif	Logo	P-value
1	1	0.926
10	10	0.233
100	100	0.988
101	101	0.709
102	102	0.783
103	103	0.368
104	104	0.694
105	105	0.598
106	106	0.0642
107	107	0.63
108	108	0.769
109	109	0.635
11	11	0.966
110	110	0.764
111	111	0.936
112	112	0.23
113	113	0.743
114	114	0.178
115	115	0.82
116	116	0.555
117	117	1.3316e-4
118	118	0.142
119	119	0.69
12	12	0.545
120	120	0.359
121	121	0.204
122	122	0.582
123	123	0.207
124	124	0.397
125	125	0.904
126	126	0.74
127	127	0.942
128	128	0.128
129	129	0.656
13	13	0.00301
130	130	0.67
131	131	0.145
132	132	0.43
133	133	0.148
134	134	0.811
135	135	0.568
136	136	0.0729
137	137	0.00552
138	138	0.975
139	139	0.604
14	14	0.513
140	140	0.757
141	141	0.485
142	142	0.524
143	143	0.31
144	144	0.926
145	145	0.548
146	146	0.538
147	147	0.696
148	148	0.173
149	149	0.199
15	15	0.171
150	150	0.781
151	151	0.644
152	152	0.154
153	153	0.233
154	154	0.707
155	155	0.628
156	156	0.0754
157	157	0.882
158	158	0.026
159	159	0.724
160	160	0.0741
161	161	0.473
162	162	0.441
163	163	0.0715
164	164	0.0502
165	165	0.159
166	166	0.183
167	167	0.385
168	168	0.183
169	169	0.191
17	17	0.817
18	18	0.892
19	19	0.0922
2	2	0.0175
20	20	0.0217
21	21	0.77
22	22	0.936
23	23	0.437
24	24	0.0607
25	25	0.661
26	26	0.0918
27	27	0.439
28	28	0.602
29	29	0.213
3	3	0.541
30	30	0.213
31	31	0.489
32	32	0.032
33	33	0.158
34	34	0.73
35	35	0.827
36	36	0.258
37	37	0.0627
38	38	0.672
39	39	0.348
4	4	0.461
40	40	0.438
41	41	0.0732
42	42	0.559
43	43	0.899
44	44	0.931
45	45	0.739
46	46	0.967
47	47	0.672
48	48	0.728
49	49	0.959
5	5	0.91
50	50	0.642
51	51	0.665
52	52	0.732
53	53	0.78
54	54	0.58
55	55	0.918
56	56	0.906
57	57	0.568
58	58	0.273
59	59	0.802
6	6	0.87
60	60	0.491
61	61	0.301
62	62	0.324
63	63	0.56
64	64	0.529
65	65	0.949
66	66	0.375
67	67	0.841
68	68	0.614
69	69	0.601
7	7	0.72
70	70	0.51
71	71	0.347
72	72	0.431
73	73	0.0348
74	74	0.332
75	75	0.00883
76	76	0.109
77	77	0.00563
78	78	0.209
79	79	0.596
8	8	0.969
80	80	0.562
81	81	0.727
82	82	0.127
83	83	0.0114
84	84	0.621
85	85	0.101
86	86	0.157
87	87	0.0123
88	88	0.431
89	89	0.254
9	9	0.69
90	90	0.493
91	91	0.55
92	92	0.399
93	93	0.252
94	94	0.913
95	95	0.00232
96	96	0.386
97	97	0.906
98	98	0.88
99	99	0.0454

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: CNhs12536

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000021 hematopoietic stem cell sample
FF:0000103 mouse 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)
0000034 (stem cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000021 (hematopoietic stem cell sample)
0000103 (mouse sample)
0000001 (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
NA

@@ Line 1: / Line 1: @@
 {{f5samples
 |DRA_sample_Accession=CAGE@SAMD00005934
-|accession_numbers=CAGE;DRX008786;DRR009658;DRZ001083;DRZ002468
+|accession_numbers=CAGE;DRX008786;DRR009658;DRZ001083;DRZ002468;DRZ012433;DRZ013818
 |ancestors_in_anatomy_facet=
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000034
@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
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@@ Line 44: / Line 44: @@
 |is_obsolete=
 |library_id=CNhs12536
-|library_id_phase_based=1:CNhs12536
+|library_id_phase_based=2:CNhs12536
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12127
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12127
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/stem%2520cell%2520%2528cKit%252b%2520Sca1-%2520lineage-%2529%2520KSL%252c%2520biol_rep3.CNhs12536.12127-128D3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/stem%2520cell%2520%2528cKit%252b%2520Sca1-%2520lineage-%2529%2520KSL%252c%2520biol_rep3.CNhs12536.12127-128D3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/stem%2520cell%2520%2528cKit%252b%2520Sca1-%2520lineage-%2529%2520KSL%252c%2520biol_rep3.CNhs12536.12127-128D3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/stem%2520cell%2520%2528cKit%252b%2520Sca1-%2520lineage-%2529%2520KSL%252c%2520biol_rep3.CNhs12536.12127-128D3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/stem%2520cell%2520%2528cKit%252b%2520Sca1-%2520lineage-%2529%2520KSL%252c%2520biol_rep3.CNhs12536.12127-128D3.mm9.nobarcode.rdna.fa.gz
 |name=stem cell (cKit+ Sca1- lineage-) KSL, biol_rep3
 |namespace=FANTOM5
@@ Line 50: / Line 59: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12536,LSID920,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.089686310701852,0,0,0,0.105986777695408,0,-0.140425304415395,0,0,0,0,-0.0843392403965415,0,0,0,0,0.052993388847704,0,-0.0859065731871663,0,0.114071786979541,0,0,0,0,0,0,0,0,0,0,0,-0.070860287599356,0,0,0,0,0,0.0516953747712841,-0.0827861207422691,-0.062922129220496,-0.984211366477826,-0.0417250640512691,0,0,0,0,0,0,0,0,0,0,0,0,-0.00978697628638479,0,0,0,0,0,0,-0.0166247784712456,0,0.105986777695408,0,-0.117389802908326,0.196016641119445,-0.101872471494027,-0.0451299367301466,0,0,-0.0760168881589905,0,0.262261155392021,0,-0.0529446460269506,-0.153063719310393,-0.539696309463514,0.0718020347797121,0,0,0,0,0,0,-0.263779565128373,-0.800642480914088,-0.194486187421589,0,0,0,0,0
@@ Line 87: / Line 96: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12127-128D3;search_select_hide=table117:12127-128D3
 }}

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FF:12127-128D3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:31, 4 June 2020

CNhs12536

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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