FF:1035-18D5: Difference between revisions

Revision as of 09:39, 28 November 2014

Name:	stomach, embryo E17
Species:	Mouse (Mus musculus)
Library ID:	CNhs11006
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	C57BL/6J
tissue	stomach
dev stage	17 days embryo
sex	mixture
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005724

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11006		CAGE		DRX009094		DRR009968

Accession ID Mm9

Library id		BAM		CTSS
CNhs11006		DRZ001393		DRZ002776

Download raw sequence, BAM & CTSS

Mm9

BAM	CTSS
[{{{mm9bam}}} download]	[{{{mm9ctss}}} donwload]

Mm10

BAM	CTSS
[{{{mm10bam}}} download]	[{{{mm10ctss}}} 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

CNhs11006

0	0
1	0
10	0
100	0
1000	0.152
1001	0.0365
1002	0.505
1003	0.0399
1004	0
1005	0.0825
1006	-0.151
1007	0.0354
1008	0
1009	0.111
101	0.0456
1010	0.0825
1011	0.0462
1012	0
1013	0.0425
1014	0.627
1015	0.074
1016	0.157
1017	1.09
1018	0.427
1019	0
102	0
1020	0
1021	0
1022	-0.0704
1023	0
1024	0.0561
1025	0.862
1026	0.053
1027	0.0908
1028	0
1029	0.391
103	0.311
1030	0.0825
1031	0.365
1032	0.103
1033	0.00724
1034	0.0655
1035	0
1036	0.147
1037	0
1038	0.0245
1039	-0.0782
104	0
1040	0.0578
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: CNhs11006

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0554
MA0003.1	MA0003.1	0.56
MA0004.1	MA0004.1	0.19
MA0006.1	MA0006.1	0.101
MA0007.1	MA0007.1	0.782
MA0009.1	MA0009.1	0.0523
MA0014.1	MA0014.1	0.977
MA0017.1	MA0017.1	0.0363
MA0018.2	MA0018.2	1.97629e-6
MA0019.1	MA0019.1	0.181
MA0024.1	MA0024.1	0.232
MA0025.1	MA0025.1	8.61966e-5
MA0027.1	MA0027.1	0.059
MA0028.1	MA0028.1	1.62471e-4
MA0029.1	MA0029.1	0.52
MA0030.1	MA0030.1	0.764
MA0031.1	MA0031.1	0.541
MA0035.2	MA0035.2	0.205
MA0038.1	MA0038.1	0.745
MA0039.2	MA0039.2	0.0386
MA0040.1	MA0040.1	0.628
MA0041.1	MA0041.1	0.139
MA0042.1	MA0042.1	0.307
MA0043.1	MA0043.1	1.20495e-4
MA0046.1	MA0046.1	0.00275
MA0047.2	MA0047.2	0.00617
MA0048.1	MA0048.1	0.0963
MA0050.1	MA0050.1	0.00323
MA0051.1	MA0051.1	1.77101e-5
MA0052.1	MA0052.1	2.35314e-4
MA0055.1	MA0055.1	0.883
MA0057.1	MA0057.1	0.079
MA0058.1	MA0058.1	0.0135
MA0059.1	MA0059.1	0.262
MA0060.1	MA0060.1	0.887
MA0061.1	MA0061.1	0.856
MA0062.2	MA0062.2	3.32671e-11
MA0065.2	MA0065.2	0.0822
MA0066.1	MA0066.1	0.984
MA0067.1	MA0067.1	0.0308
MA0068.1	MA0068.1	0.102
MA0069.1	MA0069.1	0.146
MA0070.1	MA0070.1	0.753
MA0071.1	MA0071.1	0.00108
MA0072.1	MA0072.1	0.0526
MA0073.1	MA0073.1	0.652
MA0074.1	MA0074.1	0.987
MA0076.1	MA0076.1	9.85564e-6
MA0077.1	MA0077.1	0.709
MA0078.1	MA0078.1	0.197
MA0079.2	MA0079.2	0.828
MA0080.2	MA0080.2	9.52272e-5
MA0081.1	MA0081.1	1.41243e-4
MA0083.1	MA0083.1	2.70082e-7
MA0084.1	MA0084.1	0.807
MA0087.1	MA0087.1	0.334
MA0088.1	MA0088.1	0.158
MA0090.1	MA0090.1	0.234
MA0091.1	MA0091.1	0.731
MA0092.1	MA0092.1	0.123
MA0093.1	MA0093.1	0.125
MA0099.2	MA0099.2	1.71985e-4
MA0100.1	MA0100.1	0.00402
MA0101.1	MA0101.1	0.085
MA0102.2	MA0102.2	0.55
MA0103.1	MA0103.1	3.77306e-4
MA0104.2	MA0104.2	0.114
MA0105.1	MA0105.1	0.126
MA0106.1	MA0106.1	0.0763
MA0107.1	MA0107.1	0.101
MA0108.2	MA0108.2	0.0025
MA0111.1	MA0111.1	0.985
MA0112.2	MA0112.2	0.0679
MA0113.1	MA0113.1	0.695
MA0114.1	MA0114.1	0.174
MA0115.1	MA0115.1	0.0237
MA0116.1	MA0116.1	0.0402
MA0117.1	MA0117.1	0.024
MA0119.1	MA0119.1	0.521
MA0122.1	MA0122.1	0.243
MA0124.1	MA0124.1	0.709
MA0125.1	MA0125.1	0.429
MA0131.1	MA0131.1	0.608
MA0135.1	MA0135.1	0.637
MA0136.1	MA0136.1	1.57956e-6
MA0137.2	MA0137.2	0.127
MA0138.2	MA0138.2	0.724
MA0139.1	MA0139.1	0.466
MA0140.1	MA0140.1	0.181
MA0141.1	MA0141.1	1.68576e-4
MA0142.1	MA0142.1	0.272
MA0143.1	MA0143.1	0.238
MA0144.1	MA0144.1	0.918
MA0145.1	MA0145.1	0.0773
MA0146.1	MA0146.1	0.792
MA0147.1	MA0147.1	0.0918
MA0148.1	MA0148.1	0.00644
MA0149.1	MA0149.1	0.759
MA0150.1	MA0150.1	0.0309
MA0152.1	MA0152.1	0.0346
MA0153.1	MA0153.1	3.61198e-4
MA0154.1	MA0154.1	0.0266
MA0155.1	MA0155.1	0.294
MA0156.1	MA0156.1	5.31489e-5
MA0157.1	MA0157.1	0.868
MA0159.1	MA0159.1	0.389
MA0160.1	MA0160.1	1.27055e-4
MA0162.1	MA0162.1	0.193
MA0163.1	MA0163.1	0.0239
MA0164.1	MA0164.1	0.432
MA0258.1	MA0258.1	0.819
MA0259.1	MA0259.1	0.259

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: CNhs11006

Novel motif	Logo	P-value
1	1	0.603
10	10	0.459
100	100	0.532
101	101	0.836
102	102	0.903
103	103	0.13
104	104	0.755
105	105	0.922
106	106	0.00507
107	107	0.0204
108	108	0.712
109	109	0.983
11	11	0.634
110	110	0.532
111	111	0.941
112	112	0.69
113	113	0.125
114	114	0.244
115	115	0.938
116	116	0.204
117	117	0.467
118	118	0.172
119	119	0.801
12	12	0.734
120	120	0.401
121	121	0.284
122	122	0.502
123	123	0.466
124	124	0.502
125	125	0.817
126	126	0.167
127	127	0.758
128	128	0.0546
129	129	0.546
13	13	0.0299
130	130	0.342
131	131	0.12
132	132	0.501
133	133	0.464
134	134	0.318
135	135	0.974
136	136	0.386
137	137	0.526
138	138	0.0145
139	139	0.652
14	14	0.817
140	140	0.0488
141	141	0.421
142	142	0.521
143	143	0.235
144	144	0.291
145	145	0.212
146	146	0.486
147	147	0.545
148	148	0.75
149	149	0.728
15	15	0.231
150	150	0.48
151	151	0.884
152	152	0.164
153	153	0.714
154	154	0.907
155	155	0.962
156	156	3.31114e-6
157	157	0.675
158	158	0.681
159	159	0.0288
160	160	0.0373
161	161	0.251
162	162	0.541
163	163	0.55
164	164	0.804
165	165	0.615
166	166	0.199
167	167	0.536
168	168	0.162
169	169	0.0553
17	17	0.0623
18	18	0.362
19	19	0.0262
2	2	0.609
20	20	0.358
21	21	0.107
22	22	0.315
23	23	0.537
24	24	0.516
25	25	0.0593
26	26	0.00251
27	27	0.827
28	28	0.78
29	29	0.752
3	3	0.789
30	30	0.105
31	31	0.746
32	32	0.132
33	33	0.907
34	34	0.875
35	35	0.409
36	36	0.552
37	37	0.223
38	38	0.739
39	39	0.17
4	4	0.173
40	40	0.805
41	41	0.275
42	42	0.572
43	43	0.368
44	44	0.373
45	45	0.372
46	46	0.405
47	47	0.804
48	48	0.597
49	49	0.688
5	5	0.451
50	50	0.283
51	51	0.592
52	52	0.0382
53	53	0.34
54	54	0.627
55	55	0.89
56	56	0.532
57	57	0.529
58	58	0.934
59	59	0.684
6	6	0.133
60	60	0.0862
61	61	0.603
62	62	0.435
63	63	0.669
64	64	0.743
65	65	0.903
66	66	0.427
67	67	0.838
68	68	0.146
69	69	0.219
7	7	0.385
70	70	0.414
71	71	0.0536
72	72	0.669
73	73	0.624
74	74	0.404
75	75	0.675
76	76	0.263
77	77	0.00157
78	78	0.629
79	79	0.884
8	8	0.873
80	80	0.164
81	81	0.761
82	82	0.85
83	83	0.995
84	84	0.414
85	85	0.742
86	86	0.672
87	87	0.00199
88	88	0.141
89	89	0.865
9	9	0.177
90	90	0.658
91	91	0.795
92	92	0.206
93	93	0.231
94	94	0.51
95	95	0.591
96	96	0.293
97	97	0.583
98	98	0.548
99	99	0.0756

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: CNhs11006

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011492 mouse stomach- embryo E17 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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000945 (stomach)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010039 (food storage organ)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001041 (foregut)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000300 (mouse embryonic day 17 sample)
0011492 (mouse stomach- embryo E17 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
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr5:77543897..77543911,-!p2@Hopx!2.13!248.61!Hopx;;chr13:55932591..55932622,-!p1@Pitx1!2.04!130.68!Pitx1;;chr4:135129538..135129558,-!p1@Grhl3!1.88!110.19!Grhl3;;chr5:77543935..77543947,-!p4@Hopx!1.75!55.41!Hopx;;chr10:22539932..22539956,-!p1@Tcf21!1.66!115.83!Tcf21;;chr16:25801993..25802014,+!p1@Trp63!1.64!42.24!Trp63;;chr1:137155026..137155042,-!p1@Elf3!1.62!226.65!Elf3;;chr2:103143336..103143367,-!p1@Ehf!1.61!63.77!Ehf;;chr8:59799772..59799789,+!p1@Hand2!1.60!108.73!Hand2;;chr13:48758276..48758291,+!p1@Barx1!1.58!37.43!Barx1;;chr8:123608252..123608268,+!p1@Foxf1a!1.54!49.55!Foxf1a;;chr11:121380640..121380655,-!p1@Zfp750!1.52!52.06!Zfp750;;chr17:27865882..27865901,-!p1@Spdef!1.42!25.51!Spdef;;chr13:31650185..31650201,+!p1@Foxq1!1.41!84.47!Foxq1;;chr12:58646974..58647003,-!p1@Foxa1!1.41!33.04!Foxa1;;chr19:5560600..5560617,-!p1@Ovol1!1.40!29.06!Ovol1;;chr2:103264245..103264268,+!p2@Elf5!1.39!23.42!Elf5;;chr13:55937467..55937516,-!p3@Pitx1!1.38!23.21!Pitx1;;chr2:103143315..103143328,-!p2@Ehf!1.34!20.70!Ehf;;chr3:34548909..34548927,+!p1@Sox2!1.32!33.25!Sox2;;chr2:163332558..163332596,+!p2@Hnf4a!1.30!19.03!Hnf4a;;chr13:55932624..55932641,-!p2@Pitx1!1.30!18.82!Pitx1;;chr14:118636214..118636235,-!p1@Sox21!1.29!22.16!Sox21;;chr13:48758358..48758415,+!p2@Barx1!1.26!17.15!Barx1;;chr11:121380594..121380609,-!p2@Zfp750!1.21!26.14!Zfp750;;chr15:102865131..102865151,+!p2@Hoxc4!1.19!16.31!Hoxc4;;chr13:55937432..55937460,-!p4@Pitx1!1.18!14.22!Pitx1;;chr1:189821714..189821761,+!p1@Esrrg!1.17!25.72!Esrrg;;chr10:12810631..12810649,+!p1@Plagl1!1.14!333.08!Plagl1;;chr13:31717548..31717596,+!p1@Foxf2!1.14!25.51!Foxf2;;chr7:17647736..17647772,-!p1@Hif3a!1.12!42.86!Hif3a;;chr14:99697871..99697934,+!p1@Klf5!1.11!232.51!Klf5;;chr11:121380611..121380625,-!p3@Zfp750!1.10!14.01!Zfp750;;chr7:108966820..108966835,+!p1@Phox2a!1.08!11.08!Phox2a;;chr15:102865088..102865107,+!p1@Hoxc4!1.03!13.17!Hoxc4;;chr16:38294860..38294924,-!p1@Nr1i2!1.03!9.83!Nr1i2;;chr7:19608891..19608895,-!p1@Foxa3!1.02!12.34!Foxa3;;chr2:103264213..103264233,+!p1@Elf5!1.02!9.41!Elf5;;chr12:57796615..57796687,+!p1@Pax9!1.01!9.20!Pax9;;chr9:31720843..31720888,-!p1@Barx2!0.99!9.83!Barx2;;chr3:30408603..30408668,-!p1@Mecom!0.98!20.07!Mecom;;chr13:117099847..117099907,-!p1@Isl1!0.98!15.89!Isl1;;chr14:63864056..63864102,-!p1@Gata4!0.96!14.43!Gata4;;chr14:118636238..118636257,-!p2@Sox21!0.96!8.15!Sox21;;chr5:144951153..144951203,+!p1@Bhlha15!0.95!11.71!Bhlha15;;chr3:3508024..3508069,+!p2@Hnf4g!0.95!7.95!Hnf4g;;chr10:126778916..126778974,-!p1@Gli1!0.94!17.56!Gli1;;chr6:52163319..52163342,-!p1@Hoxa3!0.94!11.29!Hoxa3;;chr11:94981424..94981439,+!p1@Dlx3!0.94!8.78!Dlx3;;chr12:39510206..39510249,+!p3@Etv1!0.94!7.74!Etv1;;chr3:90046995..90047031,-!p2@Creb3l4!0.93!9.62!Creb3l4;;chr2:172375081..172375105,+!p1@Tfap2c!0.93!7.53!Tfap2c;;chr2:164228702..164228719,+!p1@Rbpjl!0.93!7.53!Rbpjl;;chr3:34548946..34548972,+!p2@Sox2!0.92!8.15!Sox2;;chr10:88969376..88969395,-!p1@Nr1h4!0.92!7.32!Nr1h4;;chr11:96880072..96880079,+!p1@Sp6!0.92!7.32!Sp6;;chr17:86087592..86087615,-!p1@Six2!0.92!7.32!Six2;;chr2:180069370..180069409,-!p1@Gata5!0.89!7.95!Gata5;;chr13:40829137..40829205,-!p1@Tfap2a!0.88!7.53!Tfap2a;;chr4:55545337..55545357,-!p1@Klf4!0.87!99.32!Klf4;;chr3:29911808..29911833,-!p8@Mecom!0.87!6.48!Mecom;;chr5:67490284..67490302,-!p1@Phox2b!0.87!6.48!Phox2b;;chr6:14851440..14851497,+!p2@Foxp2!0.86!15.89!Foxp2;;chr11:69468531..69468557,+!p1@Sox15!0.86!6.27!Sox15;;chr7:6649134..6649167,-!p1@Zim1!0.85!34.71!Zim1;;chr4:135129447..135129467,-!p2@Grhl3!0.85!7.53!Grhl3;;chr13:31650026..31650045,+!p2@Foxq1!0.84!10.25!Foxq1;;chr6:86619104..86619119,-!p1@Mxd1!0.83!50.60!Mxd1;;chr10:44178521..44178557,-!p1@Prdm1!0.82!10.45!Prdm1;;chr15:102839948..102839975,+!p3@Hoxc6!0.81!5.44!Hoxc6;;chr14:118635860..118635885,-!p3@Sox21!0.81!5.44!Sox21;;chr10:119913310..119913366,-!p1@Hmga2!0.80!44.54!Hmga2;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.79!21.75!Ppp1r13l;;chr13:72766250..72766273,+!p1@Irx2!0.79!8.36!Irx2;;chr6:52167459..52167492,-!p1@Hoxa7!0.79!6.27!Hoxa7;;chr19:5560570..5560582,-!p2@Ovol1!0.79!5.23!Ovol1;;chr1:194979315..194979359,+!p1@Irf6!0.78!33.66!Irf6;;chr3:30408384..30408431,-!p4@Mecom!0.78!6.48!Mecom;;chr1:170361991..170362015,-!p6@Pbx1!0.77!11.71!Pbx1;;chr18:76219118..76219155,+!p1@Zbtb7c!0.77!8.99!Zbtb7c;;chr11:96153767..96153822,+!p1@Hoxb6!0.77!7.95!Hoxb6;;chr10:86956396..86956411,-!p1@Ascl1!0.76!7.74!Ascl1;;chr11:121381087..121381108,-!p4@Zfp750!0.76!4.81!Zfp750;;chr9:31720746..31720762,-!p4@Barx2!0.76!4.81!Barx2;;chr13:40826961..40827001,-!p4@Tfap2a!0.75!4.60!Tfap2a;;chr12:25257265..25257294,+!p2@Grhl1!0.75!4.60!Grhl1;;chr12:39507680..39507715,+!p2@Etv1!0.74!9.41!Etv1;;chr4:148178559..148178603,+!p1@Casz1!0.73!13.80!Casz1;;chr6:52114821..52114828,-!p1@Hoxa2!0.73!6.90!Hoxa2;;chr15:102844431..102844445,+!p1@Hoxc5!0.73!4.39!Hoxc5;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.72!7.74!Hoxb2;;chr15:37162834..37162849,+!p2@Grhl2!0.72!5.23!Grhl2;;chr7:38554763.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@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11006
-|library_id_phase_based=1:CNhs11006
+|library_id_phase_based=2:CNhs11006
 |name=stomach, embryo E17
 |namespace=FANTOM5
@@ Line 51: / Line 51: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11006,LSID730,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.167367731177939,0,0,0,0,0,0.320803751709188,0,0.0824580172145032,0,0,1.08591741417509,0,0,0,0,0,0,0.326616806163243,0,0,0,0,0,0,0,0.012717780615956,0,0,0,0,0,0.303269828250157,0,0.0824580172145032,0,0.151730312771305,0.0121213886627577,0.0921930919455012,0.0601722947155985,0.0345296691353794,0.773524308926578,0.324218378116369,0,0,0,0,0,0,0,0,0,0,0,0.151730312771305,0.0857247652078642,0,0,0,0,0.0396110621316284,0,0,0.0824580172145032,0,0.067391072374763,0.146777833772215,0.116300591087257,0.301571990121831,0.111705460871523,0,0.0824580172145032,0.00216198949518187,-0.026341265574037,0.211458253644874,0,0.0387331334221735,-0.0257027667601126,-0.20434149950279,0.185124617502552,0,0,0,0,0,0,-0.0242031415100821,0.164688854527704,0.0387030916929946,0.0300624688890411,0,0,0,0

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FF:1035-18D5: Difference between revisions

From FANTOM5_SSTAR

Revision as of 09:39, 28 November 2014

CNhs11006

	FAQ
	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0