FF:11817-124E8: Difference between revisions

Latest revision as of 18:22, 4 June 2020

Name:	CD4+CD25-CD44- naive conventional T cells, pool2 (Balb_cAJcl)
Species:	Mouse (Mus musculus)
Library ID:	CNhs13220
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	Balb/cAJcl
tissue	blood
dev stage	NA
sex	NA
age	NA
cell type	T cell
cell line	NA
company	NA
collaboration	Morikawa (University of Kyoto)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	BLnT
catalog number	NA
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005686

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13220		CAGE		DRX008796		DRR009668

Accession ID Mm9

Library id		BAM		CTSS
CNhs13220		DRZ001093		DRZ002478

Accession ID Mm10

Library id		BAM		CTSS
CNhs13220		DRZ012443		DRZ013828

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

CNhs13220

0	0
1	0
10	0
100	0
1000	-0.0173
1001	-0.0631
1002	-0.116
1003	-0.157
1004	0
1005	0
1006	-0.254
1007	-0.265
1008	0
1009	-0.19
101	0.185
1010	0
1011	0.0364
1012	0
1013	-0.139
1014	-0.0874
1015	-0.202
1016	-0.594
1017	0
1018	0
1019	0
102	0.636
1020	0.0364
1021	0.124
1022	-0.137
1023	0.0364
1024	-0.14
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.089
103	-0.0887
1030	0
1031	-1.111
1032	-0.659
1033	0.515
1034	0
1035	0
1036	0.293
1037	0
1038	-0.223
1039	-0.229
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: CNhs13220

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	4.71356e-5
MA0003.1	MA0003.1	0.274
MA0004.1	MA0004.1	0.0488
MA0006.1	MA0006.1	0.493
MA0007.1	MA0007.1	0.365
MA0009.1	MA0009.1	0.803
MA0014.1	MA0014.1	0.736
MA0017.1	MA0017.1	0.983
MA0018.2	MA0018.2	5.23107e-4
MA0019.1	MA0019.1	0.698
MA0024.1	MA0024.1	0.676
MA0025.1	MA0025.1	0.792
MA0027.1	MA0027.1	0.926
MA0028.1	MA0028.1	4.47163e-8
MA0029.1	MA0029.1	0.256
MA0030.1	MA0030.1	0.293
MA0031.1	MA0031.1	0.00665
MA0035.2	MA0035.2	0.728
MA0038.1	MA0038.1	0.00204
MA0039.2	MA0039.2	0.354
MA0040.1	MA0040.1	0.294
MA0041.1	MA0041.1	0.0512
MA0042.1	MA0042.1	0.397
MA0043.1	MA0043.1	0.0297
MA0046.1	MA0046.1	2.37414e-9
MA0047.2	MA0047.2	0.143
MA0048.1	MA0048.1	0.293
MA0050.1	MA0050.1	1.56882e-8
MA0051.1	MA0051.1	1.69982e-6
MA0052.1	MA0052.1	0.0142
MA0055.1	MA0055.1	0.144
MA0057.1	MA0057.1	0.846
MA0058.1	MA0058.1	0.0316
MA0059.1	MA0059.1	0.019
MA0060.1	MA0060.1	3.53943e-4
MA0061.1	MA0061.1	6.26951e-5
MA0062.2	MA0062.2	9.73059e-24
MA0065.2	MA0065.2	0.756
MA0066.1	MA0066.1	0.072
MA0067.1	MA0067.1	0.0923
MA0068.1	MA0068.1	0.0997
MA0069.1	MA0069.1	0.689
MA0070.1	MA0070.1	0.684
MA0071.1	MA0071.1	0.913
MA0072.1	MA0072.1	0.0895
MA0073.1	MA0073.1	0.904
MA0074.1	MA0074.1	0.273
MA0076.1	MA0076.1	1.67357e-11
MA0077.1	MA0077.1	0.143
MA0078.1	MA0078.1	0.574
MA0079.2	MA0079.2	0.0675
MA0080.2	MA0080.2	1.16197e-13
MA0081.1	MA0081.1	0.00318
MA0083.1	MA0083.1	0.135
MA0084.1	MA0084.1	0.602
MA0087.1	MA0087.1	0.878
MA0088.1	MA0088.1	0.645
MA0090.1	MA0090.1	0.0789
MA0091.1	MA0091.1	0.752
MA0092.1	MA0092.1	0.745
MA0093.1	MA0093.1	0.0598
MA0099.2	MA0099.2	0.441
MA0100.1	MA0100.1	0.138
MA0101.1	MA0101.1	3.43622e-5
MA0102.2	MA0102.2	0.82
MA0103.1	MA0103.1	0.135
MA0104.2	MA0104.2	0.0372
MA0105.1	MA0105.1	1.00043e-6
MA0106.1	MA0106.1	0.867
MA0107.1	MA0107.1	7.88025e-5
MA0108.2	MA0108.2	3.80426e-6
MA0111.1	MA0111.1	0.227
MA0112.2	MA0112.2	0.125
MA0113.1	MA0113.1	0.237
MA0114.1	MA0114.1	0.334
MA0115.1	MA0115.1	0.745
MA0116.1	MA0116.1	0.0162
MA0117.1	MA0117.1	0.501
MA0119.1	MA0119.1	0.566
MA0122.1	MA0122.1	0.522
MA0124.1	MA0124.1	0.642
MA0125.1	MA0125.1	0.154
MA0131.1	MA0131.1	0.487
MA0135.1	MA0135.1	0.834
MA0136.1	MA0136.1	1.00843e-26
MA0137.2	MA0137.2	1.1018e-4
MA0138.2	MA0138.2	0.00606
MA0139.1	MA0139.1	0.248
MA0140.1	MA0140.1	0.335
MA0141.1	MA0141.1	0.924
MA0142.1	MA0142.1	0.346
MA0143.1	MA0143.1	0.573
MA0144.1	MA0144.1	0.0202
MA0145.1	MA0145.1	0.265
MA0146.1	MA0146.1	0.791
MA0147.1	MA0147.1	0.0161
MA0148.1	MA0148.1	0.126
MA0149.1	MA0149.1	0.111
MA0150.1	MA0150.1	0.624
MA0152.1	MA0152.1	0.732
MA0153.1	MA0153.1	1.26494e-5
MA0154.1	MA0154.1	0.187
MA0155.1	MA0155.1	0.603
MA0156.1	MA0156.1	1.03144e-30
MA0157.1	MA0157.1	0.00633
MA0159.1	MA0159.1	0.155
MA0160.1	MA0160.1	0.899
MA0162.1	MA0162.1	0.977
MA0163.1	MA0163.1	0.00999
MA0164.1	MA0164.1	0.276
MA0258.1	MA0258.1	0.0939
MA0259.1	MA0259.1	0.194

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: CNhs13220

Novel motif	Logo	P-value
1	1	0.267
10	10	0.0248
100	100	0.552
101	101	0.9
102	102	0.483
103	103	0.318
104	104	0.868
105	105	0.85
106	106	0.976
107	107	0.449
108	108	0.543
109	109	0.246
11	11	0.243
110	110	0.0622
111	111	0.0663
112	112	0.0828
113	113	0.613
114	114	0.112
115	115	0.666
116	116	0.75
117	117	3.27666e-4
118	118	0.21
119	119	0.812
12	12	0.22
120	120	0.0494
121	121	0.442
122	122	0.77
123	123	0.307
124	124	0.297
125	125	0.249
126	126	0.299
127	127	0.759
128	128	0.784
129	129	0.349
13	13	0.118
130	130	0.738
131	131	0.313
132	132	0.965
133	133	0.928
134	134	0.698
135	135	0.779
136	136	0.293
137	137	0.445
138	138	0.393
139	139	0.335
14	14	0.654
140	140	0.532
141	141	0.0804
142	142	0.392
143	143	1.13569e-4
144	144	0.419
145	145	0.148
146	146	0.932
147	147	0.544
148	148	0.231
149	149	0.301
15	15	0.0813
150	150	0.732
151	151	0.292
152	152	0.232
153	153	0.479
154	154	0.248
155	155	0.0908
156	156	0.891
157	157	0.93
158	158	0.0511
159	159	0.834
160	160	0.445
161	161	0.105
162	162	0.601
163	163	0.832
164	164	0.0165
165	165	0.873
166	166	0.423
167	167	0.0758
168	168	0.631
169	169	0.769
17	17	0.635
18	18	0.25
19	19	0.144
2	2	0.0462
20	20	0.0122
21	21	0.101
22	22	0.789
23	23	0.689
24	24	0.269
25	25	0.142
26	26	0.281
27	27	0.904
28	28	0.228
29	29	0.0193
3	3	0.26
30	30	0.125
31	31	0.737
32	32	0.231
33	33	0.0873
34	34	0.438
35	35	0.0352
36	36	0.0323
37	37	0.133
38	38	0.534
39	39	0.576
4	4	0.966
40	40	0.411
41	41	0.275
42	42	0.243
43	43	0.566
44	44	0.602
45	45	0.447
46	46	0.418
47	47	0.516
48	48	0.255
49	49	0.224
5	5	0.0338
50	50	0.591
51	51	0.792
52	52	0.0732
53	53	0.731
54	54	0.629
55	55	0.441
56	56	0.904
57	57	0.639
58	58	0.344
59	59	0.795
6	6	0.646
60	60	0.974
61	61	0.183
62	62	0.0718
63	63	0.718
64	64	0.823
65	65	0.439
66	66	0.143
67	67	0.578
68	68	0.847
69	69	0.852
7	7	0.449
70	70	0.0114
71	71	0.0955
72	72	0.482
73	73	0.26
74	74	0.686
75	75	0.00566
76	76	0.0143
77	77	0.14
78	78	0.135
79	79	0.823
8	8	0.481
80	80	0.195
81	81	0.836
82	82	0.2
83	83	0.0724
84	84	0.675
85	85	0.99
86	86	0.174
87	87	0.971
88	88	0.416
89	89	0.96
9	9	0.928
90	90	0.0674
91	91	0.863
92	92	0.468
93	93	0.194
94	94	0.3
95	95	0.0922
96	96	0.191
97	97	0.507
98	98	0.45
99	99	0.0884

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: CNhs13220

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011451 CD4-positiveCD25-CD44- naive conventional T cells- (Balb_cAJcl) 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)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000791 (mature alpha-beta T cell)
0000084 (T cell)
0000789 (alpha-beta T cell)
0002419 (mature T cell)
0000624 (CD4-positive, alpha-beta T cell)
0000898 (naive T cell)
0000895 (naive thymus-derived CD4-positive, alpha-beta T cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000343 (control treatment sample)
0011451 (CD4-positiveCD25-CD44- naive conventional T cells- (Balb_cAJcl) 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)
CL:0000051 (common lymphoid progenitor)
CL:0000790 (immature alpha-beta T cell)
CL:0002425 (early T lineage precursor)
CL:0002427 (resting double-positive thymocyte)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008686
+|DRA_sample_Accession=CAGE@SAMD00005686
+|accession_numbers=CAGE;DRX008796;DRR009668;DRZ001093;DRZ002478;DRZ012443;DRZ013828
 |ancestors_in_anatomy_facet=
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0002371,CL:0000542,CL:0000219,CL:0000738,CL:0002087,CL:0002242,CL:0000255,CL:0000791,CL:0000084,CL:0000789,CL:0002419,CL:0000624,CL:0000898,CL:0000895
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr3:130815703..130815721,+!p2@Lef1!2.32!252.30!Lef1;;chr5:134720044..134720103,-!p6@Gtf2i!2.10!124.75!Gtf2i;;chr11:52096066..52096081,-!p2@Tcf7!2.08!144.68!Tcf7;;chr11:11590117..11590138,+!p4@Ikzf1!1.97!91.53!Ikzf1;;chr17:51971932..51971958,-!p2@Satb1!1.96!120.99!Satb1;;chr11:11590140..11590187,+!p3@Ikzf1!1.95!105.17!Ikzf1;;chr1:38721792..38721845,-!p1@Aff3!1.82!79.73!Aff3;;chr17:51971960..51971979,-!p1@Satb1!1.80!82.18!Satb1;;chr11:11584970..11585030,+!p2@Ikzf1!1.77!81.83!Ikzf1;;chr1:52065454..52065495,+!p1@Stat4!1.71!81.21!Stat4;;chr16:92826249..92826325,-!p1@Runx1!1.70!116.53!Runx1;;chr4:63064364..63064384,-!p1@Akna!1.68!133.32!Akna;;chr6:99216488..99216534,-!p2@Foxp1!1.66!123.87!Foxp1;;chr11:100683839..100683890,-!p2@Stat5b!1.65!99.75!Stat5b;;chr2:173044380..173044432,-!p1@Zbp1!1.63!96.51!Zbp1;;chr11:52095821..52095836,-!p3@Tcf7!1.63!41.44!Tcf7;;chr11:52096804..52096896,-!p1@Tcf7!1.61!304.14!Tcf7;;chr12:109242266..109242295,-!p1@Bcl11b!1.56!283.94!Bcl11b;;chr4:48058129..48058179,+!p2@Nr4a3!1.54!62.07!Nr4a3;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.53!41.26!Zbtb11;;chr1:52065508..52065522,+!p2@Stat4!1.50!35.93!Stat4;;chr3:130813200..130813252,+!p1@Lef1!1.49!129.38!Lef1;;chr4:124805061..124805087,-!p1@Zc3h12a!1.45!82.61!Zc3h12a;;chr8:87502608..87502623,-!p1@Junb!1.41!387.80!Junb;;chr12:86814833..86814846,+!p1@Fos!1.40!535.89!Fos;;chr11:11585912..11585950,+!p6@Ikzf1!1.40!30.33!Ikzf1;;chr2:9800207..9800234,-!p1@Gata3!1.34!62.94!Gata3;;chr7:19895384..19895399,-!p2@Fosb!1.32!27.71!Fosb;;chr11:11590085..11590106,+!p7@Ikzf1!1.32!20.02!Ikzf1;;chr14:79915425..79915501,+!p1@Elf1!1.31!169.07!Elf1;;chr11:11585678..11585745,+!p5@Ikzf1!1.31!28.41!Ikzf1;;chr9:32503590..32503680,+!p1@Ets1!1.30!665.44!Ets1;;chr11:53583544..53583559,+!p1@Irf1!1.30!307.28!Irf1;;chr11:11586218..11586285,+!p1@Ikzf1!1.30!59.80!Ikzf1;;chr1:52176315..52176343,+!p1@Stat1!1.29!255.35!Stat1;;chr8:74842952..74842970,+!p1@Klf2!1.28!1180.44!Klf2;;chr2:91077034..91077078,-!p2@Ddb2!1.28!40.04!Ddb2;;chr4:48058016..48058032,+!p3@Nr4a3!1.28!30.33!Nr4a3;;chr17:51972530..51972571,-!p7@Satb1!1.27!17.66!Satb1;;chr2:173044357..173044377,-!p2@Zbp1!1.26!24.83!Zbp1;;chr6:99216360..99216372,-!p8@Foxp1!1.26!17.40!Foxp1;;chr6:99216375..99216395,-!p5@Foxp1!1.25!16.78!Foxp1;;chr4:134708451..134708469,+!p1@Runx3!1.24!29.02!Runx3;;chr7:19895354..19895369,-!p1@Fosb!1.22!21.24!Fosb;;chr3:89191054..89191070,-!p5@Zbtb7b!1.22!15.74!Zbtb7b;;chr7:31208285..31208312,+!p3@Nfkbid!1.21!16.70!Nfkbid;;chr17:51971991..51972003,-!p4@Satb1!1.21!15.30!Satb1;;chr1:36364590..36364608,+!p1@Arid5a!1.18!141.18!Arid5a;;chr3:89191004..89191022,-!p4@Zbtb7b!1.17!13.90!Zbtb7b;;chr12:77470718..77470752,-!p4@Zbtb25!1.15!18.71!Zbtb25;;chr1:87546583..87546595,+!p1@Sp100!1.15!18.62!Sp100;;chr11:98407264..98407295,-!p1@Ikzf3!1.13!12.41!Ikzf3;;chr11:98407234..98407259,-!p2@Ikzf3!1.10!11.54!Ikzf3;;chr8:108583550..108583595,+!p2@Nfatc3!1.08!49.57!Nfatc3;;chr13:30841099..30841116,+!p1@Irf4!1.08!17.31!Irf4;;chr12:87027663..87027678,+!p2@Batf!1.07!10.67!Batf;;chr4:6917606..6917681,-!p1@Tox!1.06!43.89!Tox;;chr1:87546602..87546617,+!p2@Sp100!1.06!12.41!Sp100;;chr11:11590188..11590200,+!p8@Ikzf1!1.05!10.32!Ikzf1;;chr11:100683794..100683805,-!p4@Stat5b!1.05!10.23!Stat5b;;chr10:13685585..13685645,+!p2@Hivep2!1.04!34.79!Hivep2;;chr17:51972438..51972463,-!p8@Satb1!1.04!9.97!Satb1;;chr12:87027598..87027652,+!p1@Batf!1.03!22.38!Batf;;chr7:31206743..31206761,+!p1@Nfkbid!1.03!13.29!Nfkbid;;chr9:32348943..32349001,-!p1@Fli1!1.02!79.20!Fli1;;chr6:99385340..99385362,-!p11@Foxp1!1.02!9.35!Foxp1;;chr17:51965903..51965926,-!p5@Satb1!1.02!9.35!Satb1;;chr4:134708909..134708939,+!p3@Runx3!1.02!9.35!Runx3;;chr1:52065530..52065548,+!p3@Stat4!1.01!9.18!Stat4;;chr4:32325688..32325777,+!p1@Bach2!1.00!80.95!Bach2;;chr12:109241728..109241781,-!p2@Bcl11b!1.00!9.62!Bcl11b;;chr1:64579145..64579168,+!p6@Creb1!1.00!9.00!Creb1;;chr18:80904854..80904919,-!p2@Nfatc1!0.98!104.73!Nfatc1;;chr2:91077082..91077122,-!p1@Ddb2!0.98!54.46!Ddb2;;chr2:168415815..168415872,-!p1@Nfatc2!0.98!47.38!Nfatc2;;chr3:52072329..52072346,+!p1@Foxo1!0.96!127.11!Foxo1;;chr2:126501799..126501832,-!p4@Gabpb1!0.96!8.04!Gabpb1;;chr17:51972603..51972624,-!p9@Satb1!0.95!7.96!Satb1;;chrX:137077716..137077734,-!p1@Tsc22d3!0.94!57.78!Tsc22d3;;chr17:45692642..45692663,+!p1@Nfkbie!0.94!25.26!Nfkbie;;chr10:67000609..67000625,+!p1@Egr2!0.94!18.10!Egr2;;chr4:63064395..63064410,-!p2@Akna!0.94!13.64!Akna;;chr3:130813254..130813263,+!p4@Lef1!0.94!7.69!Lef1;;chr12:56593574..56593592,-!p1@Nfkbia!0.93!402.31!Nfkbia;;chr7:148452314..148452329,-!p1@Irf7!0.93!53.68!Irf7;;chr11:11590205..11590216,+!p9@Ikzf1!0.92!7.34!Ikzf1;;chr16:55822241..55822258,-!p1@Nfkbiz!0.91!231.14!Nfkbiz;;chr4:124805092..124805135,-!p2@Zc3h12a!0.89!29.81!Zc3h12a;;chr17:34784073..34784118,+!p2@Atf6b!0.89!28.32!Atf6b;;chr11:62272010..62272050,-!p2@Ncor1!0.89!22.99!Ncor1;;chr18:5594197..5594228,+!p7@Zeb1!0.89!6.82!Zeb1;;chr18:75527009..75527027,+!p1@Smad7!0.88!144.33!Smad7;;chr18:3337249..3337274,-!p17@Crem!0.88!6.64!Crem;;chr11:100800901..100800921,-!p4@Stat3!0.87!7.61!Stat3;;chr17:51972400..51972428,-!p11@Satb1!0.87!6.47!Satb1;;chr18:3281750..3281776,-!p2@Crem!0.86!13.20!Crem;;chr4:94718861..94718872,-!p2@Jun!0.85!48.26!Jun;;chr2:126501847..126501876,-!p5@Gabpb1!0.85!6.99!Gabpb1;;chr4:48058102..48058110,+!p5@Nr4a3!0.85!6.91!Nr4a3;;chr3:135354384..135354443,-!p1@Nfkb1!0.84!38.73!Nfkb1;;chr11:23670953..23671028,-!p1@Rel!0.84!36.19!Rel;;chr18:75527210..75527215,+!p4@Smad7!0.84!10.40!Smad7;;chr11:52096750..52096772,-!p4@Tcf7!0.84!9.35!Tcf7;;chr7:71083428..71083518,-!p3@Klf13!0.83!47.64!Klf13;;chr11:100721761..100721851,+!p1@Stat5a!0.83!45.63!Stat5a;;chr10:30375579..30375616,-!p3@Ncoa7!0.83!14.42!Ncoa7;;chr1:87497610..87497645,+!p1@Gm2427,p1@Sp140!0.83!5.77!Sp140;;chrX:45807329..45807370,-!p1@Elf4!0.82!42.40!Elf4;;chr1:133904901..133904934,+!p3@Elk4!0.82!17.48!Elk4;;chr8:47825166..47825178,+!p2@Irf2!0.82!9.00!Irf2;;chr5:92391466..92391471,+!p2@Thap6!0.82!8.39!Thap6;;chr13:44829403..44829438,+!p11@Jarid2!0.82!6.56!Jarid2;;chr12:85534957..85535017,-!p2@C130039O16Rik!0.81!29.20!C130039O16Rik;;chr7:71083729..71083742,-!p4@Klf13!0.81!10.05!Klf13;;chr2:91076997..91077012,-!p4@Ddb2!0.81!5.51!Ddb2;;chr19:26681929..26681987,+!p4@Smarca2!0.80!32.00!Smarca2;;chr5:145962698..145962742,-!p1@Zkscan14!0.80!26.84!Zkscan14;;chrX:137077653..137077669,-!p3@Tsc22d3!0.80!25.53!Tsc22d3;;chr1:87546619..87546627,+!p3@Sp100!0.80!5.25!Sp100;;chr1:133904946..133904974,+!p7@Elk4!0.79!8.13!Elk4;;chr12:109241852..109241873,-!p4@Bcl11b!0.79!6.29!Bcl11b;;chr18:3337339..3337397,-!p5@Crem!0.78!10.58!Crem;;chr3:130815472..130815497,+!p6@Lef1!0.78!5.07!Lef1;;chr17:51965928..51965960,-!p10@Satb1!0.78!4.98!Satb1;;chr15:101097270..101097290,+!p1@Nr4a1!0.77!54.55!Nr4a1;;chr18:75528166..75528170,+!p3@Smad7!0.77!13.38!Smad7;;chr19:46379199..46379301,+!p1@Nfkb2!0.76!29.64!Nfkb2;;chr15:57526345..57526392,+!p3@Zhx2!0.76!9.18!Zhx2;;chr8:108582687..108582734,+!p4@Nfatc3!0.76!4.81!Nfatc3;;chr17:51972575..51972595,-!p13@Satb1!0.76!4.72!Satb1;;chr17:84587279..84587294,-!p1@Zfp36l2!0.75!542.53!Zfp36l2;;chr4:48058047..48058062,+!p1@Nr4a3!0.75!7.34!Nr4a3;;chr17:88840082..88840127,+!p1@Foxn2!0.74!35.32!Foxn2;;chr3:52072315..52072327,+!p2@Foxo1!0.74!31.38!Foxo1;;chr16:55973950..55973977,+!p4@Rpl24,p4@Zbtb11!0.74!22.99!Zbtb11;;chr15:79178060..79178074,+!p2@Maff!0.74!6.12!Maff;;chr11:98407340..98407359,-!p4@Ikzf3!0.74!4.46!Ikzf3;;chr14:56223010..56223067,+!p1@Irf9!0.73!38.46!Irf9;;chr4:87678709..87678726,-!p4@Mllt3!0.73!14.86!Mllt3;;chr18:75527030..75527055,+!p2@Smad7!0.72!29.72!Smad7;;chr3:52072296..52072310,+!p3@Foxo1!0.72!23.69!Foxo1;;chr8:74405624..74405679,+!p3@Zfp709!0.72!7.87!Zfp709;;chr15:79178029..79178044,+!p4@Maff!0.72!5.42!Maff;;chr11:52096732..52096741,-!p6@Tcf7!0.72!4.28!Tcf7;;chr1:92949999..92950097,+!p1@Lrrfip1!0.71!124.57!Lrrfip1;;chr5:140267510..140267555,+!p2@Mafk!0.71!10.58!Mafk;;chr9:57684520..57684612,-!p1@Arid3b!0.70!40.39!Arid3b;;chrX:137077608..137077619,-!p6@Tsc22d3!0.70!5.68!Tsc22d3;;chr9:51021788..51021802,+!p1@Pou2af1!0.70!4.90!Pou2af1;;chrX:7541292..7541317,-!p3@Gata1!0.70!4.02!Gata1;;chr2:181100154..181100181,+!p3@Zgpat!0.69!22.03!Zgpat;;chr5:22940353..22940372,+!p3@Mll5!0.69!8.22!Mll5;;chr2:165818215..165818226,+!p4@Ncoa3!0.69!8.04!Ncoa3;;chr1:38721779..38721790,-!p6@Aff3!0.69!3.85!Aff3;;chr11:106134241..106134320,-!p2@Smarcd2!0.68!50.35!Smarcd2;;chr10:13686783..13686814,+!p4@Hivep2!0.68!8.48!Hivep2;;chr14:79915502..79915514,+!p4@Elf1!0.68!6.12!Elf1;;chr12:86815639..86815664,+!p2@Fos!0.68!3.76!Fos;;chr12:85560016..85560038,-!p6@C130039O16Rik!0.68!3.76!C130039O16Rik;;chr11:98407142..98407159,-!p5@Ikzf3!0.68!3.76!Ikzf3;;chr17:84587167..84587239,-!p2@Zfp36l2!0.67!14.16!Zfp36l2;;chr15:57526206..57526241,+!p2@Zhx2!0.67!13.73!Zhx2;;chr4:94718879..94718898,-!p1@Jun!0.66!298.37!Jun;;chr5:138187195..138187255,+!p1@Tsc22d4!0.66!178.51!Tsc22d4;;chr12:119539843..119539899,-!p1@Sp4!0.66!22.12!Sp4;;chr11:98407370..98407395,-!p3@Ikzf3!0.66!3.58!Ikzf3;;chr1:38721767..38721778,-!p5@Aff3!0.66!3.58!Aff3;;chr12:85559785..85559840,-!p1@C130039O16Rik!0.65!53.76!C130039O16Rik;;chr12:109241804..109241823,-!p5@Bcl11b!0.65!3.50!Bcl11b;;chr19:28085485..28085544,-!p5@Rfx3!0.64!15.12!Rfx3;;chr12:85559762..85559778,-!p5@C130039O16Rik!0.64!5.86!C130039O16Rik;;chr12:109241411..109241422,-!p8@Bcl11b!0.64!3.32!Bcl11b;;chr3:130813833..130813848,+!p16@Lef1!0.64!3.32!Lef1;;chr17:21625946..21626024,+!p1@Zfp53!0.63!42.05!Zfp53;;chr6:134780163..134780197,+!p2@Crebl2!0.63!8.57!Crebl2;;chr11:98407210..98407221,-!p7@Ikzf3!0.63!3.23!Ikzf3;;chr11:98407164..98407177,-!p8@Ikzf3!0.63!3.23!Ikzf3;;chr13:5860776..5860796,+!p1@Klf6!0.62!92.58!Klf6;;chr3:87945895..87945946,+!p2@Mef2d!0.62!11.80!Mef2d;;chr4:87679193..87679219,-!p5@Mllt3!0.62!10.05!Mllt3;;chr17:31701800..31701818,+!p2@Pknox1!0.62!9.18!Pknox1;;chr1:74634691..74634719,-!p2@Zfp142!0.62!8.83!Zfp142;;chr6:92041489..92041500,+!p4@Nr2c2!0.62!6.21!Nr2c2;;chr15:61818593..61818614,+!p4@Myc!0.62!5.94!Myc;;chr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2f4!0.25!44.76!E2f4;;chr6:92041430..92041460,+!p1@Nr2c2!0.25!36.19!Nr2c2;;chr6:83391606..83391658,-!p1@Tet3!0.25!26.66!Tet3;;chr15:102034070..102034124,+!p1@Zfp740!0.25!26.66!Zfp740;;chr11:96838974..96839007,-!p1@Sp2!0.25!24.65!Sp2;;chr7:48888915..48888973,+!p1@Zfp788!0.25!19.67!Zfp788;;chr17:24592210..24592290,-!p1@E4f1!0.25!15.74!E4f1;;chr17:46693107..46693137,-!p1@Srf!0.25!15.21!Srf;;chr10:75495343..75495405,+!p1@Zfp280b!0.25!12.85!Zfp280b;;chr16:98073403..98073460,-!p1@Prdm15!0.25!11.98!Prdm15;;chr4:133801494..133801519,-!p2@Zfp593!0.25!10.75!Zfp593;;chr15:100382390..100382441,-!p1@Tfcp2!0.25!10.14!Tfcp2;;chr16:33380950..33380988,+!p2@Zfp148!0.25!5.94!Zfp148;;chr7:134170541..134170569,-!p9@Maz!0.25!5.42!Maz;;chr7:25101609..25101678,-!p1@Zfp94!0.25!5.25!Zfp94;;chr9:20297135..20297154,-!p2@Zfp426!0.25!5.07!Zfp426;;chr2:164737086..164737108,-!p2@Zfp335!0.25!5.07!Zfp335;;chr6:124959016..124959061,+!p3@Zfp384!0.25!3.50!Zfp384;;chr3:152059025..152059046,+!p4@Gm8261,p4@Zzz3!0.25!3.32!Zzz3;;chr7:134550289..134550313,-!p1@Zfp764!0.25!3.06!Zfp764;;chr16:3744146..3744157,+!p3@Zfp263!0.25!2.88!Zfp263;;chr16:4559721..4559747,-!p3@Tfap4!0.25!2.80!Tfap4;;chr13:67229127..67229153,+!p2@Zfp759!0.25!2.36!Zfp759;;chr5:65194709..65194716,+!p10@Klf3!0.25!2.36!Klf3;;chr5:34530519..34530545,-!p4@Mxd4!0.25!1.66!Mxd4;;chr16:92826232..92826245,-!p4@Runx1!0.25!0.79!Runx1;;chr11:23670827..23670846,-!p3@Rel!0.25!0.79!Rel;;chr11:100721640..100721658,+!p2@Stat5a!0.25!0.79!Stat5a;;chr11:11589947..11589950,+!p18@Ikzf1!0.25!0.79!Ikzf1;;chr12:77470660..77470671,-!p8@Zbtb25!0.25!0.79!Zbtb25;;chr1:15795720..15795756,+!p1@Terf1!0.24!45.46!Terf1;;chr17:4995902..4995959,+!p1@Arid1b!0.24!36.98!Arid1b;;chr5:25004566..25004590,-!p1@Mll3!0.24!35.75!Mll3;;chr2:32218524..32218662,+!p1@Ciz1!0.24!35.41!Ciz1;;chr9:30837968..30838036,+!p1@Zbtb44!0.24!26.58!Zbtb44;;chr6:122769906..122769956,+!p1@Foxj2!0.24!25.70!Foxj2;;chr11:80196801..80196806,+!p2@Zfp207!0.24!22.73!Zfp207;;chr6:47870583..47870635,+!p1@Zfp212!0.24!19.15!Zfp212;;chr7:4967068..4967111,+!p1@Zfp524!0.24!16.78!Zfp524;;chr3:94819338..94819384,-!p1@Zfp687!0.24!14.16!Zfp687;;chr1:162964925..162964963,-!p1@Zbtb37!0.24!9.70!Zbtb37;;chr5:139060892..139060911,-!p2@Zfp68!0.24!6.91!Zfp68;;chr19:28086045..28086080,-!p4@Rfx3!0.24!6.82!Rfx3;;chr7:135020060..135020124,-!p2@Zfp668!0.24!6.12!Zfp668;;chrX:45947787..45947812,-!p3@Zfp280c!0.24!2.36!Zfp280c;;chrX:7339674..7339688,+!p6@Tfe3!0.24!1.66!Tfe3;;chr3:130813736..130813752,+!p3@Lef1!0.24!1.40!Lef1;;chr12:85534690..85534708,-!p9@C130039O16Rik!0.24!1.31!C130039O16Rik;;chr4:102787067..102787080,+!p10@Mier1!0.24!1.14!Mier1;;chr2:156022443..156022511,+!p1@Phf20!0.23!39.16!Phf20;;chr11:102180255..102180318,-!p1@Ubtf!0.23!34.27!Ubtf;;chr19:41557122..41557178,+!p1@Lcor!0.23!31.73!Lcor;;chr6:120314112..120314181,+!p1@Kdm5a!0.23!29.11!Kdm5a;;chr17:31701694..31701799,+!p1@Pknox1!0.23!16.26!Pknox1;;chr10:127707602..127707633,+!p1@Stat2!0.23!13.03!Stat2;;chr9:31088110..31088151,+!p1@Prdm10!0.23!9.97!Prdm10;;chr18:80909801..80909819,-!p1@Nfatc1!0.23!8.48!Nfatc1;;chr7:30644985..30645072,+!p1@Zfp420!0.23!8.39!Zfp420;;chr10:80600749..80600766,+!p2@Zbtb7a!0.23!7.34!Zbtb7a;;chr6:115803317..115803361,-!p2@Mbd4!0.23!3.06!Mbd4;;chr7:135020412..135020433,+!p2@Zfp646!0.23!3.06!Zfp646;;chr6:140572352..140572382,+!p3@Aebp2!0.23!2.62!Aebp2;;chr9:72380594..72380635,+!p3@Rfx7!0.23!1.92!Rfx7;;chr6:83391584..83391595,-!p2@Tet3!0.23!1.84!Tet3;;chr10:127080091..127080100,+!p4@Stat6!0.23!1.40!Stat6;;chr10:44178493..44178520,-!p3@Prdm1!0.23!1.31!Prdm1;;chr4:128483422..128483430,-!p6@Zfp362!0.23!1.05!Zfp362;;chr4:102792066..102792069,+!p14@Mier1!0.23!0.70!Mier1;;chr11:52096305..52096328,-!p11@Tcf7!0.23!0.70!Tcf7;;chrX:137077530..137077533,-!p11@Tsc22d3!0.23!0.70!Tsc22d3;;chr7:31208324..31208333,+!p7@Nfkbid!0.23!0.70!Nfkbid;;chr12:78063165..78063227,-!p1@Max!0.22!126.50!Max;;chr17:15636872..15636923,+!p1@Tbp!0.22!56.74!Tbp;;chr11:60034052..60034134,-!p2@Srebf1!0.22!35.23!Srebf1;;chr18:76401546..76401613,+!p1@Smad2!0.22!31.38!Smad2;;chr10:80040030..80040072,-!p1@Klf16!0.22!29.46!Klf16;;chr11:82577834..82577875,+!p1@Zfp830!0.22!29.20!Zfp830;;chr15:102236700..102236764,+!p1@Sp1!0.22!22.03!Sp1;;chrX:35542957..35543003,+!p1@Zbtb33!0.22!14.95!Zbtb33;;chr19:26679654..26679675,+!p1@Smarca2!0.22!13.38!Smarca2;;chr3:95238432..95238455,+!p2@Arnt!0.22!7.87!Arnt;;chr8:72520162..72520197,-!p4@Gatad2a!0.22!7.08!Gatad2a;;chr7:6124098..6124133,+!p1@Zfp444!0.22!6.03!Zfp444;;chr8:4613182..4613207,+!p2@Zfp958!0.22!5.25!Zfp958;;chr10:41995430..41995458,-!p3@Foxo3!0.22!3.15!Foxo3;;chr13:67229155..67229187,+!p1@Zfp759!0.22!2.88!Zfp759;;chr2:128793085..128793116,+!p2@Zc3h6!0.22!2.88!Zc3h6;;chrX:103124736..103124747,-!p6@Atrx!0.22!1.92!Atrx;;chr18:3337399..3337422,-!p11@Crem!0.22!1.66!Crem;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.22!1.31!Carhsp1;;chr4:32325445..32325468,+!p4@Bach2!0.22!1.31!Bach2;;chr9:19426719..19426729,+!p4@Zfp317!0.22!1.22!Zfp317;;chr18:35721854..35721914,+!p1@Matr3!0.21!108.75!Matr3;;c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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011451
 |is_obsolete=
-|library_ids=CNhs13220
+|library_id=CNhs13220
+|library_id_phase_based=2:CNhs13220
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11817
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11817
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13220.11817-124E8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13220.11817-124E8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13220.11817-124E8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13220.11817-124E8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13220.11817-124E8.mm9.nobarcode.rdna.fa.gz
 |name=CD4+CD25-CD44- naive conventional T cells, pool2 (Balb_cAJcl)
 |namespace=
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13220,LSID1005,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0.478663047661051,0.272816866037826,0,-0.0867151295219042,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.0616620205128307,0,0,0,0,0.465865787981125,0,0,0,0,0,0,0,0.0730988870206987,-0.178442070381905,0,0,0,0,-0.0114748003651693,0.172632698520594,-0.065606012337531,0.145772175228908,-0.984211366477826,-0.269868638010351,0.157487597443535,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0.0363974770700186,0.0363974770700186,0,-0.0824002918446139,-0.127516843312847,-0.158091042771083,0.0285229561880185,0,0,-0.157740139058892,0,0,0,-0.0839684538371419,-0.105370330788217,0.0218332385519222,-0.00885257271248303,0.0255898101063229,0,0,0,0,0,0.0143353675302104,-0.0131004605435563,0.43392170876732,0,0,0.0363974770700186,0.0811569736501016,0
@@ Line 61: / Line 73: @@
 |rna_rin=
 |rna_sample_type=total RNA
-|rna_tube_id=124E8
+|rna_tube_id=1.24E+10
 |rna_weight_ug=3.32833
 |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=table111:11817-124E8;search_select_hide=table117:11817-124E8
-|DRA_sample_Accession=CAGE@DRS008686
-|accession_numbers=DRX008796;DRR009668;DRZ001093;DRZ002478;CAGE
-|library_id=CNhs13220
 }}

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Latest revision as of 18:22, 4 June 2020

CNhs13220

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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