FF:11813-124E4: Difference between revisions

Latest revision as of 18:22, 4 June 2020

Name:	CD4+CD25-CD44- naive conventional T cells, pool1 (C57BL_6J)
Species:	Mouse (Mus musculus)
Library ID:	CNhs13217
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
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	B6nT
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		SAMD00005225

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13217		CAGE		DRX008795		DRR009667

Accession ID Mm9

Library id		BAM		CTSS
CNhs13217		DRZ001092		DRZ002477

Accession ID Mm10

Library id		BAM		CTSS
CNhs13217		DRZ012442		DRZ013827

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

CNhs13217

0	0
1	0
10	0
100	0
1000	-0.00116
1001	-0.0287
1002	-0.116
1003	-0.141
1004	0
1005	0.0686
1006	-0.143
1007	-0.181
1008	0
1009	-0.19
101	0.205
1010	0
1011	0.0686
1012	0
1013	-0.101
1014	-0.0874
1015	-0.123
1016	-0.594
1017	0
1018	0
1019	0
102	0.694
1020	0.148
1021	0.0649
1022	-0.124
1023	0
1024	-0.307
1025	0
1026	0
1027	-0.048
1028	0
1029	-0.115
103	-0.0887
1030	0
1031	-1.148
1032	-0.683
1033	0.405
1034	0
1035	0
1036	0.416
1037	0
1038	-0.154
1039	-0.184
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: CNhs13217

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	2.27047e-5
MA0003.1	MA0003.1	0.262
MA0004.1	MA0004.1	0.0589
MA0006.1	MA0006.1	0.442
MA0007.1	MA0007.1	0.245
MA0009.1	MA0009.1	0.672
MA0014.1	MA0014.1	0.725
MA0017.1	MA0017.1	0.878
MA0018.2	MA0018.2	0.00117
MA0019.1	MA0019.1	0.613
MA0024.1	MA0024.1	0.684
MA0025.1	MA0025.1	0.589
MA0027.1	MA0027.1	0.918
MA0028.1	MA0028.1	4.67099e-8
MA0029.1	MA0029.1	0.0807
MA0030.1	MA0030.1	0.3
MA0031.1	MA0031.1	0.0053
MA0035.2	MA0035.2	0.888
MA0038.1	MA0038.1	0.00614
MA0039.2	MA0039.2	0.342
MA0040.1	MA0040.1	0.32
MA0041.1	MA0041.1	0.0673
MA0042.1	MA0042.1	0.503
MA0043.1	MA0043.1	0.0498
MA0046.1	MA0046.1	3.63424e-10
MA0047.2	MA0047.2	0.139
MA0048.1	MA0048.1	0.334
MA0050.1	MA0050.1	4.43777e-10
MA0051.1	MA0051.1	2.78516e-7
MA0052.1	MA0052.1	0.00911
MA0055.1	MA0055.1	0.134
MA0057.1	MA0057.1	0.889
MA0058.1	MA0058.1	0.0481
MA0059.1	MA0059.1	0.0244
MA0060.1	MA0060.1	5.23444e-4
MA0061.1	MA0061.1	8.67915e-5
MA0062.2	MA0062.2	1.01941e-23
MA0065.2	MA0065.2	0.858
MA0066.1	MA0066.1	0.134
MA0067.1	MA0067.1	0.0779
MA0068.1	MA0068.1	0.0251
MA0069.1	MA0069.1	0.962
MA0070.1	MA0070.1	0.914
MA0071.1	MA0071.1	0.941
MA0072.1	MA0072.1	0.0916
MA0073.1	MA0073.1	0.803
MA0074.1	MA0074.1	0.408
MA0076.1	MA0076.1	3.52052e-11
MA0077.1	MA0077.1	0.102
MA0078.1	MA0078.1	0.56
MA0079.2	MA0079.2	0.0551
MA0080.2	MA0080.2	5.54865e-14
MA0081.1	MA0081.1	0.00305
MA0083.1	MA0083.1	0.176
MA0084.1	MA0084.1	0.798
MA0087.1	MA0087.1	0.913
MA0088.1	MA0088.1	0.68
MA0090.1	MA0090.1	0.0886
MA0091.1	MA0091.1	0.642
MA0092.1	MA0092.1	0.727
MA0093.1	MA0093.1	0.076
MA0099.2	MA0099.2	0.46
MA0100.1	MA0100.1	0.166
MA0101.1	MA0101.1	1.3357e-5
MA0102.2	MA0102.2	0.781
MA0103.1	MA0103.1	0.159
MA0104.2	MA0104.2	0.0433
MA0105.1	MA0105.1	2.28159e-6
MA0106.1	MA0106.1	0.948
MA0107.1	MA0107.1	4.49873e-5
MA0108.2	MA0108.2	2.48672e-5
MA0111.1	MA0111.1	0.208
MA0112.2	MA0112.2	0.0977
MA0113.1	MA0113.1	0.31
MA0114.1	MA0114.1	0.345
MA0115.1	MA0115.1	0.56
MA0116.1	MA0116.1	0.0283
MA0117.1	MA0117.1	0.446
MA0119.1	MA0119.1	0.507
MA0122.1	MA0122.1	0.411
MA0124.1	MA0124.1	0.455
MA0125.1	MA0125.1	0.121
MA0131.1	MA0131.1	0.385
MA0135.1	MA0135.1	0.925
MA0136.1	MA0136.1	9.63199e-28
MA0137.2	MA0137.2	2.24288e-4
MA0138.2	MA0138.2	0.00614
MA0139.1	MA0139.1	0.3
MA0140.1	MA0140.1	0.569
MA0141.1	MA0141.1	0.985
MA0142.1	MA0142.1	0.2
MA0143.1	MA0143.1	0.577
MA0144.1	MA0144.1	0.0231
MA0145.1	MA0145.1	0.215
MA0146.1	MA0146.1	0.744
MA0147.1	MA0147.1	0.0215
MA0148.1	MA0148.1	0.173
MA0149.1	MA0149.1	0.11
MA0150.1	MA0150.1	0.784
MA0152.1	MA0152.1	0.904
MA0153.1	MA0153.1	1.38088e-5
MA0154.1	MA0154.1	0.359
MA0155.1	MA0155.1	0.483
MA0156.1	MA0156.1	1.12574e-31
MA0157.1	MA0157.1	0.00374
MA0159.1	MA0159.1	0.164
MA0160.1	MA0160.1	0.938
MA0162.1	MA0162.1	0.833
MA0163.1	MA0163.1	0.0101
MA0164.1	MA0164.1	0.301
MA0258.1	MA0258.1	0.0624
MA0259.1	MA0259.1	0.13

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: CNhs13217

Novel motif	Logo	P-value
1	1	0.248
10	10	0.0278
100	100	0.596
101	101	0.868
102	102	0.512
103	103	0.277
104	104	0.929
105	105	0.887
106	106	0.98
107	107	0.413
108	108	0.426
109	109	0.215
11	11	0.256
110	110	0.0484
111	111	0.103
112	112	0.11
113	113	0.398
114	114	0.117
115	115	0.724
116	116	0.668
117	117	4.83597e-4
118	118	0.206
119	119	0.688
12	12	0.232
120	120	0.0779
121	121	0.489
122	122	0.925
123	123	0.375
124	124	0.342
125	125	0.252
126	126	0.396
127	127	0.69
128	128	0.724
129	129	0.277
13	13	0.0573
130	130	0.841
131	131	0.446
132	132	0.899
133	133	0.834
134	134	0.489
135	135	0.803
136	136	0.344
137	137	0.334
138	138	0.383
139	139	0.313
14	14	0.669
140	140	0.228
141	141	0.171
142	142	0.266
143	143	2.16595e-4
144	144	0.495
145	145	0.0841
146	146	0.908
147	147	0.388
148	148	0.3
149	149	0.377
15	15	0.0762
150	150	0.724
151	151	0.194
152	152	0.239
153	153	0.256
154	154	0.189
155	155	0.143
156	156	0.465
157	157	0.941
158	158	0.0581
159	159	0.605
160	160	0.439
161	161	0.08
162	162	0.397
163	163	0.706
164	164	0.0278
165	165	0.611
166	166	0.56
167	167	0.0811
168	168	0.68
169	169	0.731
17	17	0.677
18	18	0.29
19	19	0.164
2	2	0.0434
20	20	0.0156
21	21	0.0849
22	22	0.703
23	23	0.72
24	24	0.316
25	25	0.121
26	26	0.308
27	27	0.878
28	28	0.28
29	29	0.024
3	3	0.233
30	30	0.107
31	31	0.694
32	32	0.236
33	33	0.0803
34	34	0.404
35	35	0.0489
36	36	0.0415
37	37	0.151
38	38	0.517
39	39	0.436
4	4	0.937
40	40	0.447
41	41	0.299
42	42	0.219
43	43	0.516
44	44	0.692
45	45	0.435
46	46	0.404
47	47	0.521
48	48	0.286
49	49	0.2
5	5	0.0394
50	50	0.563
51	51	0.82
52	52	0.0625
53	53	0.727
54	54	0.663
55	55	0.546
56	56	0.872
57	57	0.567
58	58	0.262
59	59	0.639
6	6	0.578
60	60	0.943
61	61	0.151
62	62	0.0642
63	63	0.76
64	64	0.863
65	65	0.472
66	66	0.239
67	67	0.624
68	68	0.996
69	69	0.853
7	7	0.384
70	70	0.00883
71	71	0.089
72	72	0.567
73	73	0.239
74	74	0.83
75	75	0.00524
76	76	0.0124
77	77	0.101
78	78	0.119
79	79	0.691
8	8	0.475
80	80	0.147
81	81	0.902
82	82	0.163
83	83	0.0439
84	84	0.591
85	85	0.939
86	86	0.188
87	87	0.925
88	88	0.434
89	89	0.767
9	9	0.958
90	90	0.0368
91	91	0.937
92	92	0.469
93	93	0.174
94	94	0.292
95	95	0.139
96	96	0.233
97	97	0.556
98	98	0.428
99	99	0.117

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: CNhs13217

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011450 CD4-positiveCD25-CD44- naive conventional T cells- (C57BL_6J) 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)
0011450 (CD4-positiveCD25-CD44- naive conventional T cells- (C57BL_6J) 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@DRS008685
+|DRA_sample_Accession=CAGE@SAMD00005225
-|accession_numbers=CAGE;DRX008795;DRR009667;DRZ001092;DRZ002477
+|accession_numbers=CAGE;DRX008795;DRR009667;DRZ001092;DRZ002477;DRZ012442;DRZ013827
 |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 9: / 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!247.04!Lef1;;chr11:52096066..52096081,-!p2@Tcf7!2.17!176.51!Tcf7;;chr5:134720044..134720103,-!p6@Gtf2i!2.14!137.30!Gtf2i;;chr11:11590117..11590138,+!p4@Ikzf1!2.00!97.93!Ikzf1;;chr17:51971932..51971958,-!p2@Satb1!1.98!128.40!Satb1;;chr11:11590140..11590187,+!p3@Ikzf1!1.98!112.14!Ikzf1;;chr11:11584970..11585030,+!p2@Ikzf1!1.84!96.39!Ikzf1;;chr1:38721792..38721845,-!p1@Aff3!1.80!77.38!Aff3;;chr17:51971960..51971979,-!p1@Satb1!1.78!78.75!Satb1;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.78!75.33!Zbtb11;;chr11:100683839..100683890,-!p2@Stat5b!1.75!123.95!Stat5b;;chr1:52065454..52065495,+!p1@Stat4!1.74!86.46!Stat4;;chr11:52095821..52095836,-!p3@Tcf7!1.74!53.93!Tcf7;;chr2:173044380..173044432,-!p1@Zbp1!1.72!119.67!Zbp1;;chr6:99216488..99216534,-!p2@Foxp1!1.69!130.80!Foxp1;;chr11:52096804..52096896,-!p1@Tcf7!1.66!343.77!Tcf7;;chr4:63064364..63064384,-!p1@Akna!1.61!111.62!Akna;;chr16:92826249..92826325,-!p1@Runx1!1.59!90.57!Runx1;;chr11:11585912..11585950,+!p6@Ikzf1!1.53!41.77!Ikzf1;;chr12:109242266..109242295,-!p1@Bcl11b!1.51!248.93!Bcl11b;;chr1:52065508..52065522,+!p2@Stat4!1.50!35.78!Stat4;;chr4:48058129..48058179,+!p2@Nr4a3!1.47!52.56!Nr4a3;;chr9:32503590..32503680,+!p1@Ets1!1.45!944.34!Ets1;;chr4:124805061..124805087,-!p1@Zc3h12a!1.40!72.59!Zc3h12a;;chr2:173044357..173044377,-!p2@Zbp1!1.40!34.58!Zbp1;;chr3:130813200..130813252,+!p1@Lef1!1.39!102.04!Lef1;;chr11:11586218..11586285,+!p1@Ikzf1!1.39!72.76!Ikzf1;;chr12:86814833..86814846,+!p1@Fos!1.37!500.08!Fos;;chr11:11585678..11585745,+!p5@Ikzf1!1.34!30.30!Ikzf1;;chr2:9800207..9800234,-!p1@Gata3!1.33!60.61!Gata3;;chr6:99216360..99216372,-!p8@Foxp1!1.33!20.54!Foxp1;;chr11:98407264..98407295,-!p1@Ikzf3!1.33!20.37!Ikzf3;;chr11:11590085..11590106,+!p7@Ikzf1!1.32!19.86!Ikzf1;;chr17:51971991..51972003,-!p4@Satb1!1.32!19.86!Satb1;;chr14:79915425..79915501,+!p1@Elf1!1.31!167.43!Elf1;;chr11:100683794..100683805,-!p4@Stat5b!1.30!18.83!Stat5b;;chr11:53583544..53583559,+!p1@Irf1!1.29!298.06!Irf1;;chr1:52176315..52176343,+!p1@Stat1!1.29!258.00!Stat1;;chr6:99216375..99216395,-!p5@Foxp1!1.29!18.32!Foxp1;;chr8:87502608..87502623,-!p1@Junb!1.27!280.26!Junb;;chr3:89191004..89191022,-!p4@Zbtb7b!1.27!17.80!Zbtb7b;;chr11:98407234..98407259,-!p2@Ikzf3!1.27!17.46!Ikzf3;;chr2:91077034..91077078,-!p2@Ddb2!1.23!34.92!Ddb2;;chr4:134708451..134708469,+!p1@Runx3!1.23!28.08!Runx3;;chr12:87027663..87027678,+!p2@Batf!1.23!15.92!Batf;;chr4:48058016..48058032,+!p3@Nr4a3!1.22!26.54!Nr4a3;;chr17:51972530..51972571,-!p7@Satb1!1.21!15.07!Satb1;;chr1:36364590..36364608,+!p1@Arid5a!1.20!147.23!Arid5a;;chr8:74842952..74842970,+!p1@Klf2!1.19!959.58!Klf2;;chr5:92391466..92391471,+!p2@Thap6!1.18!20.37!Thap6;;chr10:13685585..13685645,+!p2@Hivep2!1.17!47.25!Hivep2;;chr7:31206743..31206761,+!p1@Nfkbid!1.17!18.83!Nfkbid;;chr17:51965903..51965926,-!p5@Satb1!1.17!13.70!Satb1;;chr13:30841099..30841116,+!p1@Irf4!1.16!20.89!Irf4;;chrX:137077716..137077734,-!p1@Tsc22d3!1.15!92.96!Tsc22d3;;chr12:77470718..77470752,-!p4@Zbtb25!1.15!18.49!Zbtb25;;chr1:87546583..87546595,+!p1@Sp100!1.14!18.32!Sp100;;chr7:19895384..19895399,-!p2@Fosb!1.13!17.63!Fosb;;chr8:108583550..108583595,+!p2@Nfatc3!1.12!54.61!Nfatc3;;chr1:87546602..87546617,+!p2@Sp100!1.12!14.38!Sp100;;chr6:99385340..99385362,-!p11@Foxp1!1.12!12.16!Foxp1;;chr2:91076997..91077012,-!p4@Ddb2!1.10!11.64!Ddb2;;chr4:134708909..134708939,+!p3@Runx3!1.10!11.64!Runx3;;chr11:11590188..11590200,+!p8@Ikzf1!1.10!11.47!Ikzf1;;chr4:6917606..6917681,-!p1@Tox!1.09!47.08!Tox;;chr12:87027598..87027652,+!p1@Batf!1.09!26.19!Batf;;chr4:32325688..32325777,+!p1@Bach2!1.08!96.90!Bach2;;chr17:51972438..51972463,-!p8@Satb1!1.08!10.96!Satb1;;chr9:32348943..32349001,-!p1@Fli1!1.06!85.77!Fli1;;chr7:31208285..31208312,+!p3@Nfkbid!1.06!11.64!Nfkbid;;chr1:52065530..52065548,+!p3@Stat4!1.06!10.61!Stat4;;chr11:11590205..11590216,+!p9@Ikzf1!1.06!10.44!Ikzf1;;chr1:64579145..64579168,+!p6@Creb1!1.05!10.27!Creb1;;chr3:89191054..89191070,-!p5@Zbtb7b!1.03!9.76!Zbtb7b;;chr18:3281750..3281776,-!p2@Crem!1.02!19.35!Crem;;chr7:148452314..148452329,-!p1@Irf7!1.01!66.08!Irf7;;chr18:3337249..3337274,-!p17@Crem!1.01!9.24!Crem;;chr17:51972603..51972624,-!p9@Satb1!1.01!9.24!Satb1;;chr2:126501799..126501832,-!p4@Gabpb1!1.01!9.24!Gabpb1;;chr17:45692642..45692663,+!p1@Nfkbie!1.00!29.10!Nfkbie;;chr7:71083729..71083742,-!p4@Klf13!0.98!15.24!Klf13;;chr1:87497610..87497645,+!p1@Gm2427,p1@Sp140!0.97!8.39!Sp140;;chr3:52072329..52072346,+!p1@Foxo1!0.96!128.74!Foxo1;;chr11:52096750..52096772,-!p4@Tcf7!0.96!12.67!Tcf7;;chr3:130815472..130815497,+!p6@Lef1!0.96!8.05!Lef1;;chr12:109241728..109241781,-!p2@Bcl11b!0.95!8.56!Bcl11b;;chr18:80904854..80904919,-!p2@Nfatc1!0.94!94.16!Nfatc1;;chr2:168415815..168415872,-!p1@Nfatc2!0.94!43.31!Nfatc2;;chr1:87546619..87546627,+!p3@Sp100!0.94!7.70!Sp100;;chr11:62272010..62272050,-!p2@Ncor1!0.92!24.65!Ncor1;;chr4:63064395..63064410,-!p2@Akna!0.92!12.84!Akna;;chr7:19895354..19895369,-!p1@Fosb!0.92!10.27!Fosb;;chr19:2668192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0.68!Zfp64;;chr11:98799690..98799701,+!p17@Rara!0.23!0.68!Rara;;chr10:20881239..20881254,-!p5@Myb!0.23!0.68!Myb;;chr11:23670799..23670808,-!p7@Rel!0.23!0.68!Rel;;chr12:109241791..109241802,-!p7@Bcl11b!0.23!0.68!Bcl11b;;chr11:98407448..98407455,-!p12@Ikzf3!0.23!0.68!Ikzf3;;chr6:120314480..120314487,+!p6@Kdm5a!0.23!0.68!Kdm5a;;chr15:82742573..82742620,-!p2@Tcf20!0.23!0.68!Tcf20;;chr16:92826232..92826245,-!p4@Runx1!0.23!0.68!Runx1;;chr16:92826180..92826191,-!p5@Runx1!0.23!0.68!Runx1;;chr1:64579394..64579433,+!p1@Creb1!0.22!53.59!Creb1;;chr14:75684150..75684197,+!p1@Zc3h13!0.22!48.62!Zc3h13;;chr16:4213951..4213995,-!p@chr16:4213951..4213995,-!0.22!41.26!Crebbp;;chr6:120314112..120314181,+!p1@Kdm5a!0.22!28.08!Kdm5a;;chr9:20264394..20264448,-!p1@Zfp26!0.22!26.54!Zfp26;;chr8:74474953..74475029,+!p1@Zfp961!0.22!24.31!Zfp961;;chr11:3189883..3189925,+!p1@Patz1!0.22!20.20!Patz1;;chr7:134376741..134376831,+!p1@Zfp553!0.22!19.17!Zfp553;;chr16:23988711..23988727,-!p1@Bcl6!0.22!17.12!Bcl6;;chr17:25152711..25152736,-!p1@Cramp1l!0.22!14.55!Cramp1l;;chr8:109620276..109620306,-!p2@Terf2!0.22!8.05!Terf2;;chr12:110031227..110031254,+!p3@Yy1!0.22!7.88!Yy1;;chr9:21420572..21420591,+!p2@Smarca4!0.22!7.70!Smarca4;;chr11:102180696..102180760,-!p2@Ubtf!0.22!6.85!Ubtf;;chr19:12870598..12870636,-!p1@U05342,p1@Zfp91!0.22!6.85!Zfp91;;chr6:39068210..39068251,-!p1@Parp12!0.22!6.16!Parp12;;chr18:84255804..84255832,-!p2@Tshz1!0.22!4.62!Tshz1;;chr10:79896690..79896746,-!p4@Tcf3!0.22!4.45!Tcf3;;chr8:108160826..108160879,+!p3@Ctcf!0.22!3.60!Ctcf;;chr3:30500978..30501018,+!p1@Mynn!0.22!3.25!Mynn;;chr6:115803317..115803361,-!p2@Mbd4!0.22!2.91!Mbd4;;chr7:49761111..49761128,-!p2@ENSMUST00000174407,p2@uc009gmb.1!0.22!2.40!Zfp141;;chrX:131543765..131543775,-!p2@Zmat1!0.22!2.40!Zmat1;;chr7:46773162..46773172,+!p2@Zfp619!0.22!1.71!Zfp619;;chr4:102792009..102792021,+!p6@Mier1!0.22!1.71!Mier1;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.22!1.54!Ncoa4;;chr13:29045131..29045159,-!p3@Sox4!0.22!1.37!Sox4;;chr5:77695241..77695257,+!p10@Rest!0.22!0.86!Rest;;chr4:40917988..40918060,+!p1@Nfx1!0.21!99.30!Nfx1;;chr15:76307834..76307891,+!p1@Hsf1!0.21!57.52!Hsf1;;chr18:70727922..70728052,+!p1@Mbd2!0.21!53.07!Mbd2;;chr7:29551488..29551529,-!p1@Nfkbib!0.21!46.91!Nfkbib;;chr16:91044627..91044703,-!p1@Gcfc1!0.21!46.57!Gcfc1;;chr5:25004592..25004630,-!p2@Mll3!0.21!29.28!Mll3;;chr6:29997979..29998049,+!p1@Nrf1!0.21!26.36!Nrf1;;chr15:100058266..100058287,+!p1@Atf1!0.21!22.60!Atf1;;chr7:120351014..120351109,+!p1@Arntl!0.21!19.69!Arntl;;chr17:21145885..21145977,+!p1@Zfp160!0.21!19.52!Zfp160;;chr17:84105551..84105600,+!p1@Mta3!0.21!15.92!Mta3;;chr19:38893646..38893732,-!p1@Noc3l!0.21!15.24!Noc3l;;chr17:46693107..46693137,-!p1@Srf!0.21!13.52!Srf;;chr11:53164378..53164392,+!p2@Aff4!0.21!12.16!Aff4;;chr13:67552527..67552574,-!p1@Zfp874a!0.21!5.82!Zfp874a;;chr2:83484738..83484749,+!p5@Zc3h15!0.21!5.14!Zc3h15;;chr17:15701286..15701323,-!p1@Prdm9!0.21!4.96!Prdm9;;chr10:41995430..41995458,-!p3@Foxo3!0.21!3.08!Foxo3;;chr15:76181718..76181729,+!p3@Maf1!0.21!2.74!Maf1;;chr16:3744146..3744157,+!p3@Zfp263!0.21!2.57!Zfp263;;chr6:140572352..140572382,+!p3@Aebp2!0.21!2.40!Aebp2;;chr17:87153440..87153451,+!p4@Epas1!0.21!2.23!Epas1;;chr2:56967334..56967366,-!p1@Nr4a2!0.21!2.23!Nr4a2;;chr3:30993859..30993870,+!p5@Skil!0.21!1.37!Skil;;chr5:77695390..77695414,+!p2@Rest!0.21!1.03!Rest;;chr18:60720384..60720450,+!p1@Rbm22!0.20!74.30!Rbm22;;chr4:154597177..154597195,-!p1@Ski!0.20!54.96!Ski;;chr6:140571997..140572136,+!p1@Aebp2!0.20!33.38!Aebp2;;chr11:60034052..60034134,-!p2@Srebf1!0.20!33.21!Srebf1;;chr11:80196801..80196806,+!p2@Zfp207!0.20!20.37!Zfp207;;chr9:63605740..63605771,-!p1@Smad3!0.20!20.03!Smad3;;chr2:28915759..28915807,+!p1@Ttf1!0.20!19.35!Ttf1;;chr11:115891618..115891699,+!p1@Unk!0.20!17.29!Unk;;chr9:55785900..55785950,-!p1@Scaper!0.20!13.87!Scaper;;chr10:20032304..20032324,+!p2@Bclaf1!0.20!12.84!Bclaf1;;chr15:61816932..61816952,+!p2@Myc!0.20!11.13!Myc;;chr4:135841976..135842029,+!p2@Zfp46!0.20!9.93!Zfp46;;chr9:44113678..44113771,-!p1@Hinfp!0.20!9.76!Hinfp;;chr7:138554009..138554034,-!p1@Ikzf5!0.20!8.39!Ikzf5;;chr7:24919204..24919231,+!p2@Zfp235!0.20!7.19!Zfp235;;chr8:4613182..4613207,+!p2@Zfp958!0.20!4.96!Zfp958;;chr7:4866835..4866858,+!p2@Zfp628!0.20!4.79!Zfp628;;chr7:4866778..4866801,+!p3@Zfp628!0.20!4.45!Zfp628;;chr3:89197551..89197606,-!p2@Zbtb7b!0.20!4.11!Zbtb7b;;chr3:95021663..95021687,-!p3@Gabpb2!0.20!4.11!Gabpb2;;chrX:48558950..48559016,-!p1@Mbnl3!0.20!3.77!Mbnl3;;chr4:45025159..45025197,-!p1@Zbtb5!0.20!3.60!Zbtb5;;chr13:67830046..67830082,-!p2@Zfp71-rs1!0.20!3.42!Zfp71-rs1;;chr1:64167550..64167618,-!p4@Klf7!0.20!3.08!Klf7;;chr5:138187181..138187192,+!p5@Tsc22d4!0.20!2.91!Tsc22d4;;chr18:36441119..36441158,+!p2@Pura!0.20!2.74!Pura;;chr6:28211956..28211967,-!p2@Zfp800!0.20!2.23!Zfp800;;chr17:4994491..4994531,+!p6@Arid1b!0.20!2.05!Arid1b;;chr17:47874074..47874098,+!p3@Tfeb!0.20!1.88!Tfeb;;chr10:13685657..13685677,+!p7@Hivep2!0.20!1.03!Hivep2;;chr14:47896863..47896886,-!p5@Wdh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4568..107694586,+!p5@Cbfb!0.17!1.88!Cbfb;;chr13:59924354..59924366,-!p3@Zcchc6!0.17!1.71!Zcchc6;;chr9:72380594..72380635,+!p3@Rfx7!0.17!1.54!Rfx7;;chr15:25914138..25914146,+!p4@Zfp622!0.17!1.37!Zfp622;;chr5:65203599..65203617,+!p8@Klf3!0.17!1.37!Klf3;;chr16:95923586..95923598,+!p5@Ets2!0.17!0.86!Ets2;;chr5:104182943..104182954,+!p12@Aff1!0.17!0.86!Aff1;;chr1:36364572..36364580,+!p2@Arid5a!0.17!0.68!Arid5a;;chr12:81213989..81214006,-!p1@Zfp36l1!0.16!66.60!Zfp36l1;;chr5:108697948..108697999,+!p1@Dr1!0.16!40.23!Dr1;;chr11:87881744..87881791,+!p1@Vezf1!0.16!36.29!Vezf1;;chr9:113840256..113840306,+!p1@Ubp1!0.16!27.39!Ubp1;;chr7:16986536..16986582,+!p1@Zc3h4!0.16!26.54!Zc3h4;;chr1:173341474..173341513,+!p2@Usf1!0.16!17.29!Usf1;;chr11:4604645..4604705,+!p1@Zmat5!0.16!16.44!Zmat5;;chr15:96117968..96118035,+!p1@Arid2!0.16!11.47!Arid2;;chr16:4559608..4559681,-!p1@Tfap4!0.16!10.10!Tfap4;;chr9:122795920..122795977,+!p1@Zfp167!0.16!10.10!Zfp167;;chr6:47785649..47785724,+!p1@Zfp398!0.16!9.93!Zfp398;;chr7:28764174..28764200,-!p1@Zfp780b!0.16!8.05!Zfp780b;;chr10:114821807..114821852,-!p2@Thap2!0.16!8.05!Thap2;;chr19:5637528..5637548,+!p2@Rela!0.16!7.02!Rela;;chr7:134170541..134170569,-!p9@Maz!0.16!4.28!Maz;;chr17:69732364..69732405,+!p2@Zfp161!0.16!3.77!Zfp161;;chr14:52898807..52898863,+!p2@Tox4!0.16!3.08!Tox4;;chr9:113840082..113840105,+!p3@Ubp1!0.16!2.91!Ubp1;;chr2:166888481..166888548,-!p3@Znfx1!0.16!2.74!Znfx1;;chr3:94641604..94641615,+!p5@Pogz!0.16!2.05!Pogz;;chr8:72663049..72663061,-!p4@LOC100048268,p4@Rfxank!0.16!1.54!Rfxank;;chr9:96619968..96619983,-!p6@Zbtb38!0.16!1.37!Zbtb38;;chr7:135381498..135381509,-!p2@9130023H24Rik!0.16!1.37!9130023H24Rik;;chr5:138187411..138187422,+!p8@Tsc22d4!0.16!1.20!Tsc22d4;;chr15:80085678..80085693,+!p2@Atf4!0.16!1.20!Atf4;;chr6:47785727..47785738,+!p6@Zfp398!0.16!1.03!Zfp398;;chr6:72850124..72850210,-!p7@Kcmf1!0.16!0.86!Kcmf1;;chr16:55838757..55838774,-!p2@Nfkbiz!0.16!0.68!Nfkbiz;;chr11:100800621..100800633,-!p5@Stat3!0.16!0.68!Stat3;;chr7:51809271..51809325,-!p1@Nr1h2!0.15!71.22!Nr1h2;;chrX:71330925..71330991,-!p1@Mecp2!0.15!28.93!Mecp2;;chr19:47125313..47125405,-!p1@Pcgf6!0.15!26.88!Pcgf6;;chr4:120887676..120887719,-!p1@Rlf!0.15!25.68!Rlf;;chr13:21494557..21494617,-!p1@Zkscan3!0.15!23.11!Zkscan3;;chr9:30837968..30838036,+!p1@Zbtb44!0.15!21.74!Zbtb44;;chr14:22320101..22320119,+!p1@Myst4!0.15!16.95!Myst4;;chr15:81494344..81494388,+!p1@L3mbtl2!0.15!14.21!L3mbtl2;;chr18:84758883..84758919,-!p1@Zfp407!0.15!13.35!Zfp407;;chr17:34053127..34053141,+!p1@Zbtb22!0.15!13.18!Zbtb22;;chr3:94641350..94641380,+!p1@Pogz!0.15!12.16!Pogz;;chr11:95574298..95574344,+!p1@Zfp652,p4@Phospho1!0.15!10.61!Zfp652;;chr1:167932744..167932778,-!p1@Pou2f1!0.15!10.61!Pou2f1;;chr13:65380118..65380146,+!p2@Zfp369!0.15!7.88!Zfp369;;chr8:125897750..125897758,+!p2@Tcf25!0.15!7.88!Tcf25;;chr2:48805015..48805042,+!p2@Mbd5!0.15!7.02!Mbd5;;chr2:126501274..126501308,-!p2@Gabpb1!0.15!4.45!Gabpb1;;chr17:25152743..25152766,-!p2@Cramp1l!0.15!4.45!Cramp1l;;chr8:72520139..72520157,-!p6@Gatad2a!0.15!4.28!Gatad2a;;chr14:19071567..19071612,-!p2@Nr1d2!0.15!4.11!Nr1d2;;chr5:110539087..110539133,+!p1@Zfp605!0.15!3.08!Zfp605;;chr5:22939771..22939797,+!p4@Mll5!0.15!1.88!Mll5;;chr13:55206625..55206636,+!p2@Zfp346!0.15!1.71!Zfp346;;chr12:25336286..25336297,+!p2@Klf11!0.15!1.03!Klf11;;chr11:62271274..62271337,-!p4@Ncor1!0.15!1.03!Ncor1;;chr1:74634786..74634804,-!p5@Zfp142!0.15!0.86!Zfp142;;chr5:138188180..138188203,+!p12@Tsc22d4!0.15!0.68!Tsc22d4;;chr15:61818914..61818943,+!p7@Myc!0.15!0.68!Myc;;chr6:52663725..52663794,+!p1@Tax1bp1!0.14!188.32!Tax1bp1;;chr11:95171500..95171527,-!p1@Myst2!0.14!76.18!Myst2;;chr6:64992569..64992656,+!p1@Smarcad1!0.14!35.95!Smarcad1;;chr6:90319480..90319651,+!p1@Zxdc!0.14!31.67!Zxdc;;chr11:58136797..58136859,-!p1@Zfp672!0.14!29.10!Zfp672;;chrX:70587953..70587968,+!p1@Zfp275!0.14!13.01!Zfp275;;chr18:39649430..39649522,-!p2@Nr3c1!0.14!11.47!Nr3c1;;chr1:64579364..64579389,+!p2@Creb1!0.14!10.44!Creb1;;chr3:32409487..32409563,+!p1@Zfp639!0.14!8.56!Zfp639;;chr19:26679615..26679646,+!p3@Smarca2!0.14!7.88!Smarca2;;chr10:41996550..41996569,-!p2@Foxo3!0.14!4.96!Foxo3;;chr9:20297135..20297154,-!p2@Zfp426!0.14!3.77!Zfp426;;chr4:151401710..151401733,-!p2@Zbtb48!0.14!3.08!Zbtb48;;chr7:16986617..16986632,+!p2@Zc3h4!0.14!2.74!Zc3h4;;chr9:55785981..55786009,-!p2@Scaper!0.14!2.57!Scaper;;chr18:5334765..5334833,-!p2@Zfp438!0.14!2.57!Zfp438;;chr13:64253718..64253763,-!p2@Zfp367!0.14!2.40!Zfp367;;
@@ Line 44: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs13217
-|library_ids=CNhs13217
+|library_id_phase_based=2:CNhs13217
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11813
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11813
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520pool1%2520%2528C57BL_6J%2529.CNhs13217.11813-124E4.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%2520pool1%2520%2528C57BL_6J%2529.CNhs13217.11813-124E4.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%2520pool1%2520%2528C57BL_6J%2529.CNhs13217.11813-124E4.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%2520pool1%2520%2528C57BL_6J%2529.CNhs13217.11813-124E4.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%2520pool1%2520%2528C57BL_6J%2529.CNhs13217.11813-124E4.mm9.nobarcode.rdna.fa.gz
 |name=CD4+CD25-CD44- naive conventional T cells, pool1 (C57BL_6J)
 |namespace=
@@ Line 50: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13217,LSID1005,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0.459875978736811,0.127882415780397,0,-0.0679160856748575,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.123262016501424,0,0,0,0,0.180011747370744,0,0,0,0,0,0,0,0.0726401304674395,-0.216315067559074,0,0,0,0,-0.0023962426745025,0.110621137557951,-0.0661618130246221,0.200004268853529,-0.984211366477826,-0.269868638010351,0.226549106464441,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0.0203617662679788,0.0686313343811508,0,4.33811219612487e-05,0.262129394168328,-0.158091042771083,-0.0022770418062781,0,0,-0.110125607842934,-0.00688340347187388,0,0,-0.0636859831609172,-0.0261549429242535,-0.0434887023377375,-0.0788315948399074,0.00385995141019347,0,0,0,0,0,0.0237456848108339,-0.162566995096443,0.415406118486149,0,0,0,0.180011747370744,0
@@ Line 63: / Line 73: @@
 |rna_rin=
 |rna_sample_type=total RNA
-|rna_tube_id=124E4
+|rna_tube_id=1.24E+06
 |rna_weight_ug=4.6458
 |sample_age=
@@ Line 87: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11813-124E4;search_select_hide=table117:11813-124E4
 }}

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FF:11813-124E4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:22, 4 June 2020

CNhs13217

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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