Tsankov 2015, TF binding dynamics during human ES cell differentiation.

Description

This serie is part of the RoadMap consortium. It contains data for the HUES64 cell line (an embryonic stem cell) as it go through differentiation in mesoendoderm, mesoderm, endoderm and ectoderm. Several transcription factors and histone marks were analyzed at each stage of differentiation.

Source

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly.

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM1505809_CMYC_HUES64_P.sga HUES64 - CMYC - Paired-end CMYC GSM1505809
2 GSM1505621_CTCF_HUES64_P.sga HUES64 - CTCF - Paired-end CTCF GSM1505621
3 GSM1505622_CTCF_HUES64_P.sga HUES64 - CTCF - Paired-end CTCF GSM1505622
4 GSM1505620_CTCF_HUES64_S.sga HUES64 - CTCF - Single-end CTCF GSM1505620
5 GSM1505627_EOMES_HUES64_P.sga HUES64 - EOMES - Paired-end EOMES GSM1505627
6 GSM1505633_FOXA1_HUES64_P.sga HUES64 - FOXA1 - Paired-end FOXA1 GSM1505633
7 GSM1505640_FOXA2_HUES64_P.sga HUES64 - FOXA2 - Paired-end FOXA2 GSM1505640
8 GSM1505642_GATA4_HUES64_P.sga HUES64 - GATA4 - Paired-end GATA4 GSM1505642
9 GSM1505659_GATA6_HUES64_P.sga HUES64 - GATA6 - Paired-end GATA6 GSM1505659
10 GSM1505813_HAND1_HUES64_P.sga HUES64 - HAND1 - Paired-end HAND1 GSM1505813
11 GSM1505681_HNF1B_HUES64_P.sga HUES64 - HNF1B - Paired-end HNF1B GSM1505681
12 GSM1505687_HNF4A_HUES64_P.sga HUES64 - HNF4A - Paired-end HNF4A GSM1505687
13 GSM1505690_KLF5_HUES64_P.sga HUES64 - KLF5 - Paired-end KLF5 GSM1505690
14 GSM1505699_NANOG_HUES64_P.sga HUES64 - NANOG - Paired-end NANOG GSM1505699
15 GSM1505700_NANOG_HUES64_P.sga HUES64 - NANOG - Paired-end NANOG GSM1505700
16 GSM1505695_NANOG_HUES64_S.sga HUES64 - NANOG - Single-end NANOG GSM1505695
17 GSM1505698_NANOG_HUES64_S.sga HUES64 - NANOG - Single-end NANOG GSM1505698
18 GSM1505693_NR5A2_HUES64_P.sga HUES64 - NR5A2 - Paired-end NR5A2 GSM1505693
19 GSM1505709_OTX2_HUES64_P.sga HUES64 - OTX2 - Paired-end OTX2 GSM1505709
20 GSM1505711_OTX2_HUES64_P.sga HUES64 - OTX2 - Paired-end OTX2 GSM1505711
21 GSM1505712_OTX2_HUES64_P.sga HUES64 - OTX2 - Paired-end OTX2 GSM1505712
22 GSM1505704_OTX2_HUES64_S.sga HUES64 - OTX2 - Single-end OTX2 GSM1505704
23 GSM1505716_POL2_HUES64_P.sga HUES64 - POL2 - Paired-end POL2 GSM1505716
24 GSM1505717_POL2_HUES64_P.sga HUES64 - POL2 - Paired-end POL2 GSM1505717
25 GSM1505724_POU5F1_HUES64_P.sga HUES64 - POU5F1 - Paired-end POU5F1 GSM1505724
26 GSM1505725_POU5F1_HUES64_P.sga HUES64 - POU5F1 - Paired-end POU5F1 GSM1505725
27 GSM1505728_POU5F1_HUES64_S.sga HUES64 - POU5F1 - Single-end POU5F1 GSM1505728
28 GSM1505617_PRDM1_HUES64_P.sga HUES64 - PRDM1 - Paired-end PRDM1 GSM1505617
29 GSM1505731_REX1_HUES64_P.sga HUES64 - REX1 - Paired-end REX1 GSM1505731
30 GSM1505732_SALL4_HUES64_S.sga HUES64 - SALL4 - Single-end SALL4 GSM1505732
31 GSM1505745_SMAD1_HUES64_P.sga HUES64 - SMAD1 - Paired-end SMAD1 GSM1505745
32 GSM1505747_SMAD23_HUES64_S.sga HUES64 - SMAD23 - Single-end SMAD23 GSM1505747
33 GSM1505751_SMAD4_HUES64_P.sga HUES64 - SMAD4 - Paired-end SMAD4 GSM1505751
34 GSM1505757_SMAD4_HUES64_P.sga HUES64 - SMAD4 - Paired-end SMAD4 GSM1505757
35 GSM1505758_SNAI2_HUES64_P.sga HUES64 - SNAI2 - Paired-end SNAI2 GSM1505758
36 GSM1505760_SOX17_HUES64_P.sga HUES64 - SOX17 - Paired-end SOX17 GSM1505760
37 GSM1505766_SOX2_HUES64_P.sga HUES64 - SOX2 - Paired-end SOX2 GSM1505766
38 GSM1505768_SOX2_HUES64_S.sga HUES64 - SOX2 - Single-end SOX2 GSM1505768
39 GSM1505771_SP1_HUES64_P.sga HUES64 - SP1 - Paired-end SP1 GSM1505771
40 GSM1505769_SP1_HUES64_S.sga HUES64 - SP1 - Single-end SP1 GSM1505769
41 GSM1505774_SRF_HUES64_P.sga HUES64 - SRF - Paired-end SRF GSM1505774
42 GSM1505775_SRF_HUES64_P.sga HUES64 - SRF - Paired-end SRF GSM1505775
43 GSM1505772_SRF_HUES64_S.sga HUES64 - SRF - Single-end SRF GSM1505772
44 GSM1505781_STAT3_HUES64_P.sga HUES64 - STAT3 - Paired-end STAT3 GSM1505781
45 GSM1505785_TAL1_HUES64_P.sga HUES64 - TAL1 - Paired-end TAL1 GSM1505785
46 GSM1505791_TCF4_HUES64_P.sga HUES64 - TCF4 - Paired-end TCF4 GSM1505791
47 GSM1505796_THAP11_HUES64_P.sga HUES64 - THAP11 - Paired-end THAP11 GSM1505796
48 GSM1505801_TRIM28_HUES64_P.sga HUES64 - TRIM28 - Paired-end TRIM28 GSM1505801
49 GSM1505782_T_HUES64_P.sga HUES64 - T - Paired-end T GSM1505782
50 GSM1505802_WCE_HUES64_S.sga HUES64 - WCE - Single-end WCE GSM1505802
51 GSM1505803_WCE_HUES64_S.sga HUES64 - WCE - Single-end WCE GSM1505803
52 GSM1505804_WCE_HUES64_S.sga HUES64 - WCE - Single-end WCE GSM1505804
53 GSM1505808_CMYC_dEC_P.sga dEC - CMYC - Paired-end CMYC GSM1505808
54 GSM1505808_CMYC_dEC_S.sga dEC - CMYC - Single-end CMYC GSM1505808
55 GSM1505626_CTCF_dEC_P.sga dEC - CTCF - Paired-end CTCF GSM1505626
56 GSM1505703_NANOG_dEC_P.sga dEC - NANOG - Paired-end NANOG GSM1505703
57 GSM1505710_OTX2_dEC_P.sga dEC - OTX2 - Paired-end OTX2 GSM1505710
58 GSM1505707_OTX2_dEC_S.sga dEC - OTX2 - Single-end OTX2 GSM1505707
59 GSM1505715_PAX6_dEC_P.sga dEC - PAX6 - Paired-end PAX6 GSM1505715
60 GSM1505715_PAX6_dEC_S.sga dEC - PAX6 - Single-end PAX6 GSM1505715
61 GSM1505721_POL2_dEC_P.sga dEC - POL2 - Paired-end POL2 GSM1505721
62 GSM1505727_POU5F1_dEC_P.sga dEC - POU5F1 - Paired-end POU5F1 GSM1505727
63 GSM1505736_SMAD1_dEC_S.sga dEC - SMAD1 - Single-end SMAD1 GSM1505736
64 GSM1505748_SMAD23_dEC_S.sga dEC - SMAD23 - Single-end SMAD23 GSM1505748
65 GSM1505755_SMAD4_dEC_S.sga dEC - SMAD4 - Single-end SMAD4 GSM1505755
66 GSM1505778_SRF_dEC_P.sga dEC - SRF - Paired-end SRF GSM1505778
67 GSM1505790_TCF4_dEC_S.sga dEC - TCF4 - Single-end TCF4 GSM1505790
68 GSM1505792_THAP11_dEC_P.sga dEC - THAP11 - Paired-end THAP11 GSM1505792
69 GSM1505797_TRIM28_dEC_P.sga dEC - TRIM28 - Paired-end TRIM28 GSM1505797
70 GSM1505648_GATA4_dEN_shGATA4_1_P.sga dEN_shGATA4_1 - GATA4 - Paired-end GATA4 GSM1505648
71 GSM1505666_H3K27Ac_dEN_shGATA4_1_P.sga dEN_shGATA4_1 - H3K27Ac - Paired-end H3K27Ac GSM1505666
72 GSM1505738_SMAD1_dEN_shGATA4_1_P.sga dEN_shGATA4_1 - SMAD1 - Paired-end SMAD1 GSM1505738
73 GSM1505649_GATA4_dEN_shGATA4_2_P.sga dEN_shGATA4_2 - GATA4 - Paired-end GATA4 GSM1505649
74 GSM1505667_H3K27Ac_dEN_shGATA4_2_P.sga dEN_shGATA4_2 - H3K27Ac - Paired-end H3K27Ac GSM1505667
75 GSM1505739_SMAD1_dEN_shGATA4_2_P.sga dEN_shGATA4_2 - SMAD1 - Paired-end SMAD1 GSM1505739
76 GSM1505650_GATA4_dEN_shGATA4_3_P.sga dEN_shGATA4_3 - GATA4 - Paired-end GATA4 GSM1505650
77 GSM1505668_H3K27Ac_dEN_shGATA4_3_P.sga dEN_shGATA4_3 - H3K27Ac - Paired-end H3K27Ac GSM1505668
78 GSM1505740_SMAD1_dEN_shGATA4_3_P.sga dEN_shGATA4_3 - SMAD1 - Paired-end SMAD1 GSM1505740
79 GSM1505806_CMYC_dEN_P.sga dEN - CMYC - Paired-end CMYC GSM1505806
80 GSM1505806_CMYC_dEN_S.sga dEN - CMYC - Single-end CMYC GSM1505806
81 GSM1505625_CTCF_dEN_P.sga dEN - CTCF - Paired-end CTCF GSM1505625
82 GSM1505628_EOMES_dEN_P.sga dEN - EOMES - Paired-end EOMES GSM1505628
83 GSM1505629_EOMES_dEN_P.sga dEN - EOMES - Paired-end EOMES GSM1505629
84 GSM1505628_EOMES_dEN_S.sga dEN - EOMES - Single-end EOMES GSM1505628
85 GSM1505635_FOXA1_dEN_P.sga dEN - FOXA1 - Paired-end FOXA1 GSM1505635
86 GSM1505636_FOXA1_dEN_P.sga dEN - FOXA1 - Paired-end FOXA1 GSM1505636
87 GSM1505632_FOXA1_dEN_S.sga dEN - FOXA1 - Single-end FOXA1 GSM1505632
88 GSM1505639_FOXA2_dEN_P.sga dEN - FOXA2 - Paired-end FOXA2 GSM1505639
89 GSM1505641_FOXA2_dEN_P.sga dEN - FOXA2 - Paired-end FOXA2 GSM1505641
90 GSM1505637_FOXA2_dEN_S.sga dEN - FOXA2 - Single-end FOXA2 GSM1505637
91 GSM1505646_GATA4_dEN_P.sga dEN - GATA4 - Paired-end GATA4 GSM1505646
92 GSM1505647_GATA4_dEN_P.sga dEN - GATA4 - Paired-end GATA4 GSM1505647
93 GSM1505655_GATA4_dEN_P.sga dEN - GATA4 - Paired-end GATA4 GSM1505655
94 GSM1505660_GATA6_dEN_P.sga dEN - GATA6 - Paired-end GATA6 GSM1505660
95 GSM1505664_GATA6_dEN_P.sga dEN - GATA6 - Paired-end GATA6 GSM1505664
96 GSM1505658_GATA6_dEN_S.sga dEN - GATA6 - Single-end GATA6 GSM1505658
97 GSM1505665_H3K27Ac_dEN_P.sga dEN - H3K27Ac - Paired-end H3K27Ac GSM1505665
98 GSM1505683_HNF1B_dEN_P.sga dEN - HNF1B - Paired-end HNF1B GSM1505683
99 GSM1505680_HNF1B_dEN_S.sga dEN - HNF1B - Single-end HNF1B GSM1505680
100 GSM1505684_HNF4A_dEN_P.sga dEN - HNF4A - Paired-end HNF4A GSM1505684
101 GSM1505686_HNF4A_dEN_P.sga dEN - HNF4A - Paired-end HNF4A GSM1505686
102 GSM1505684_HNF4A_dEN_S.sga dEN - HNF4A - Single-end HNF4A GSM1505684
103 GSM1505688_KLF5_dEN_P.sga dEN - KLF5 - Paired-end KLF5 GSM1505688
104 GSM1505688_KLF5_dEN_S.sga dEN - KLF5 - Single-end KLF5 GSM1505688
105 GSM1505702_NANOG_dEN_P.sga dEN - NANOG - Paired-end NANOG GSM1505702
106 GSM1505696_NANOG_dEN_S.sga dEN - NANOG - Single-end NANOG GSM1505696
107 GSM1505705_OTX2_dEN_P.sga dEN - OTX2 - Paired-end OTX2 GSM1505705
108 GSM1505708_OTX2_dEN_P.sga dEN - OTX2 - Paired-end OTX2 GSM1505708
109 GSM1505705_OTX2_dEN_S.sga dEN - OTX2 - Single-end OTX2 GSM1505705
110 GSM1505714_PAX6_dEN_S.sga dEN - PAX6 - Single-end PAX6 GSM1505714
111 GSM1505720_POL2_dEN_P.sga dEN - POL2 - Paired-end POL2 GSM1505720
112 GSM1505722_POU5F1_dEN_P.sga dEN - POU5F1 - Paired-end POU5F1 GSM1505722
113 GSM1505616_PRDM1_dEN_P.sga dEN - PRDM1 - Paired-end PRDM1 GSM1505616
114 GSM1505618_PRDM1_dEN_P.sga dEN - PRDM1 - Paired-end PRDM1 GSM1505618
115 GSM1505730_REX1_dEN_P.sga dEN - REX1 - Paired-end REX1 GSM1505730
116 GSM1505734_SMAD1_dEN_P.sga dEN - SMAD1 - Paired-end SMAD1 GSM1505734
117 GSM1505737_SMAD1_dEN_P.sga dEN - SMAD1 - Paired-end SMAD1 GSM1505737
118 GSM1505734_SMAD1_dEN_S.sga dEN - SMAD1 - Single-end SMAD1 GSM1505734
119 GSM1505749_SMAD23_dEN_S.sga dEN - SMAD23 - Single-end SMAD23 GSM1505749
120 GSM1505752_SMAD4_dEN_P.sga dEN - SMAD4 - Paired-end SMAD4 GSM1505752
121 GSM1505752_SMAD4_dEN_S.sga dEN - SMAD4 - Single-end SMAD4 GSM1505752
122 GSM1505763_SOX17_dEN_P.sga dEN - SOX17 - Paired-end SOX17 GSM1505763
123 GSM1505764_SOX2_dEN_S.sga dEN - SOX2 - Single-end SOX2 GSM1505764
124 GSM1505770_SP1_dEN_P.sga dEN - SP1 - Paired-end SP1 GSM1505770
125 GSM1505773_SRF_dEN_P.sga dEN - SRF - Paired-end SRF GSM1505773
126 GSM1505773_SRF_dEN_S.sga dEN - SRF - Single-end SRF GSM1505773
127 GSM1505779_STAT3_dEN_P.sga dEN - STAT3 - Paired-end STAT3 GSM1505779
128 GSM1505787_TCF4_dEN_P.sga dEN - TCF4 - Paired-end TCF4 GSM1505787
129 GSM1505787_TCF4_dEN_S.sga dEN - TCF4 - Single-end TCF4 GSM1505787
130 GSM1505793_THAP11_dEN_P.sga dEN - THAP11 - Paired-end THAP11 GSM1505793
131 GSM1505798_TRIM28_dEN_P.sga dEN - TRIM28 - Paired-end TRIM28 GSM1505798
132 GSM1505652_GATA4_dME_shGATA4_1_P.sga dME_shGATA4_1 - GATA4 - Paired-end GATA4 GSM1505652
133 GSM1505670_H3K27Ac_dME_shGATA4_1_P.sga dME_shGATA4_1 - H3K27Ac - Paired-end H3K27Ac GSM1505670
134 GSM1505742_SMAD1_dME_shGATA4_1_P.sga dME_shGATA4_1 - SMAD1 - Paired-end SMAD1 GSM1505742
135 GSM1505653_GATA4_dME_shGATA4_2_P.sga dME_shGATA4_2 - GATA4 - Paired-end GATA4 GSM1505653
136 GSM1505671_H3K27Ac_dME_shGATA4_2_P.sga dME_shGATA4_2 - H3K27Ac - Paired-end H3K27Ac GSM1505671
137 GSM1505743_SMAD1_dME_shGATA4_2_P.sga dME_shGATA4_2 - SMAD1 - Paired-end SMAD1 GSM1505743
138 GSM1505654_GATA4_dME_shGATA4_3_P.sga dME_shGATA4_3 - GATA4 - Paired-end GATA4 GSM1505654
139 GSM1505672_H3K27Ac_dME_shGATA4_3_P.sga dME_shGATA4_3 - H3K27Ac - Paired-end H3K27Ac GSM1505672
140 GSM1505744_SMAD1_dME_shGATA4_3_P.sga dME_shGATA4_3 - SMAD1 - Paired-end SMAD1 GSM1505744
141 GSM1505619_CDX2_dME_P.sga dME - CDX2 - Paired-end CDX2 GSM1505619
142 GSM1505619_CDX2_dME_S.sga dME - CDX2 - Single-end CDX2 GSM1505619
143 GSM1505807_CMYC_dME_P.sga dME - CMYC - Paired-end CMYC GSM1505807
144 GSM1505807_CMYC_dME_S.sga dME - CMYC - Single-end CMYC GSM1505807
145 GSM1505623_CTCF_dME_P.sga dME - CTCF - Paired-end CTCF GSM1505623
146 GSM1505644_GATA4_dME_P.sga dME - GATA4 - Paired-end GATA4 GSM1505644
147 GSM1505645_GATA4_dME_P.sga dME - GATA4 - Paired-end GATA4 GSM1505645
148 GSM1505651_GATA4_dME_P.sga dME - GATA4 - Paired-end GATA4 GSM1505651
149 GSM1505656_GATA4_dME_P.sga dME - GATA4 - Paired-end GATA4 GSM1505656
150 GSM1505657_GATA4_dME_P.sga dME - GATA4 - Paired-end GATA4 GSM1505657
151 GSM1505644_GATA4_dME_S.sga dME - GATA4 - Single-end GATA4 GSM1505644
152 GSM1505661_GATA6_dME_P.sga dME - GATA6 - Paired-end GATA6 GSM1505661
153 GSM1505663_GATA6_dME_P.sga dME - GATA6 - Paired-end GATA6 GSM1505663
154 GSM1505669_H3K27Ac_dME_P.sga dME - H3K27Ac - Paired-end H3K27Ac GSM1505669
155 GSM1505812_HAND1_dME_P.sga dME - HAND1 - Paired-end HAND1 GSM1505812
156 GSM1505812_HAND1_dME_S.sga dME - HAND1 - Single-end HAND1 GSM1505812
157 GSM1505811_HAND2_dME_P.sga dME - HAND2 - Paired-end HAND2 GSM1505811
158 GSM1505679_HEY1_dME_P.sga dME - HEY1 - Paired-end HEY1 GSM1505679
159 GSM1505691_LEF1_dME_P.sga dME - LEF1 - Paired-end LEF1 GSM1505691
160 GSM1505691_LEF1_dME_S.sga dME - LEF1 - Single-end LEF1 GSM1505691
161 GSM1505697_NANOG_dME_P.sga dME - NANOG - Paired-end NANOG GSM1505697
162 GSM1505697_NANOG_dME_S.sga dME - NANOG - Single-end NANOG GSM1505697
163 GSM1505713_OTX2_dME_P.sga dME - OTX2 - Paired-end OTX2 GSM1505713
164 GSM1505718_POL2_dME_P.sga dME - POL2 - Paired-end POL2 GSM1505718
165 GSM1505723_POU5F1_dME_P.sga dME - POU5F1 - Paired-end POU5F1 GSM1505723
166 GSM1505723_POU5F1_dME_S.sga dME - POU5F1 - Single-end POU5F1 GSM1505723
167 GSM1505729_REX1_dME_P.sga dME - REX1 - Paired-end REX1 GSM1505729
168 GSM1505729_REX1_dME_S.sga dME - REX1 - Single-end REX1 GSM1505729
169 GSM1505735_SMAD1_dME_P.sga dME - SMAD1 - Paired-end SMAD1 GSM1505735
170 GSM1505741_SMAD1_dME_P.sga dME - SMAD1 - Paired-end SMAD1 GSM1505741
171 GSM1505754_SMAD4_dME_P.sga dME - SMAD4 - Paired-end SMAD4 GSM1505754
172 GSM1505756_SMAD4_dME_P.sga dME - SMAD4 - Paired-end SMAD4 GSM1505756
173 GSM1505759_SNAI2_dME_P.sga dME - SNAI2 - Paired-end SNAI2 GSM1505759
174 GSM1505759_SNAI2_dME_S.sga dME - SNAI2 - Single-end SNAI2 GSM1505759
175 GSM1505762_SOX17_dME_P.sga dME - SOX17 - Paired-end SOX17 GSM1505762
176 GSM1505765_SOX2_dME_P.sga dME - SOX2 - Paired-end SOX2 GSM1505765
177 GSM1505765_SOX2_dME_S.sga dME - SOX2 - Single-end SOX2 GSM1505765
178 GSM1505777_SRF_dME_P.sga dME - SRF - Paired-end SRF GSM1505777
179 GSM1505780_STAT3_dME_P.sga dME - STAT3 - Paired-end STAT3 GSM1505780
180 GSM1505786_TAL1_dME_P.sga dME - TAL1 - Paired-end TAL1 GSM1505786
181 GSM1505789_TCF4_dME_P.sga dME - TCF4 - Paired-end TCF4 GSM1505789
182 GSM1505789_TCF4_dME_S.sga dME - TCF4 - Single-end TCF4 GSM1505789
183 GSM1505794_THAP11_dME_P.sga dME - THAP11 - Paired-end THAP11 GSM1505794
184 GSM1505799_TRIM28_dME_P.sga dME - TRIM28 - Paired-end TRIM28 GSM1505799
185 GSM1505805_WCE_dME_S.sga dME - WCE - Single-end WCE GSM1505805
186 GSM1505810_CMYC_dMS_P.sga dMS - CMYC - Paired-end CMYC GSM1505810
187 GSM1505624_CTCF_dMS_P.sga dMS - CTCF - Paired-end CTCF GSM1505624
188 GSM1505631_EOMES_dMS_P.sga dMS - EOMES - Paired-end EOMES GSM1505631
189 GSM1505630_EOMES_dMS_S.sga dMS - EOMES - Single-end EOMES GSM1505630
190 GSM1505634_FOXA1_dMS_P.sga dMS - FOXA1 - Paired-end FOXA1 GSM1505634
191 GSM1505634_FOXA1_dMS_S.sga dMS - FOXA1 - Single-end FOXA1 GSM1505634
192 GSM1505638_FOXA2_dMS_P.sga dMS - FOXA2 - Paired-end FOXA2 GSM1505638
193 GSM1505638_FOXA2_dMS_S.sga dMS - FOXA2 - Single-end FOXA2 GSM1505638
194 GSM1505643_GATA4_dMS_P.sga dMS - GATA4 - Paired-end GATA4 GSM1505643
195 GSM1505643_GATA4_dMS_S.sga dMS - GATA4 - Single-end GATA4 GSM1505643
196 GSM1505662_GATA6_dMS_P.sga dMS - GATA6 - Paired-end GATA6 GSM1505662
197 GSM1505673_H3K27Ac_dMS_P.sga dMS - H3K27Ac - Paired-end H3K27Ac GSM1505673
198 GSM1505674_H3K27Ac_dMS_P.sga dMS - H3K27Ac - Paired-end H3K27Ac GSM1505674
199 GSM1505675_H3K27me3_dMS_P.sga dMS - H3K27me3 - Paired-end H3K27me3 GSM1505675
200 GSM1505676_H3K4me1_dMS_P.sga dMS - H3K4me1 - Paired-end H3K4me1 GSM1505676
201 GSM1505677_H3K4me3_dMS_P.sga dMS - H3K4me3 - Paired-end H3K4me3 GSM1505677
202 GSM1505678_H3K9me3_dMS_P.sga dMS - H3K9me3 - Paired-end H3K9me3 GSM1505678
203 GSM1505814_HAND1_dMS_P.sga dMS - HAND1 - Paired-end HAND1 GSM1505814
204 GSM1505682_HNF1B_dMS_P.sga dMS - HNF1B - Paired-end HNF1B GSM1505682
205 GSM1505682_HNF1B_dMS_S.sga dMS - HNF1B - Single-end HNF1B GSM1505682
206 GSM1505685_HNF4A_dMS_P.sga dMS - HNF4A - Paired-end HNF4A GSM1505685
207 GSM1505685_HNF4A_dMS_S.sga dMS - HNF4A - Single-end HNF4A GSM1505685
208 GSM1505689_KLF5_dMS_P.sga dMS - KLF5 - Paired-end KLF5 GSM1505689
209 GSM1505689_KLF5_dMS_S.sga dMS - KLF5 - Single-end KLF5 GSM1505689
210 GSM1505692_LEF1_dMS_P.sga dMS - LEF1 - Paired-end LEF1 GSM1505692
211 GSM1505701_NANOG_dMS_P.sga dMS - NANOG - Paired-end NANOG GSM1505701
212 GSM1505694_NR5A2_dMS_P.sga dMS - NR5A2 - Paired-end NR5A2 GSM1505694
213 GSM1505706_OTX2_dMS_S.sga dMS - OTX2 - Single-end OTX2 GSM1505706
214 GSM1505719_POL2_dMS_P.sga dMS - POL2 - Paired-end POL2 GSM1505719
215 GSM1505726_POU5F1_dMS_P.sga dMS - POU5F1 - Paired-end POU5F1 GSM1505726
216 GSM1505615_PRDM1_dMS_S.sga dMS - PRDM1 - Single-end PRDM1 GSM1505615
217 GSM1505733_SALL4_dMS_P.sga dMS - SALL4 - Paired-end SALL4 GSM1505733
218 GSM1505746_SMAD1_dMS_P.sga dMS - SMAD1 - Paired-end SMAD1 GSM1505746
219 GSM1505750_SMAD23_dMS_P.sga dMS - SMAD23 - Paired-end SMAD23 GSM1505750
220 GSM1505750_SMAD23_dMS_S.sga dMS - SMAD23 - Single-end SMAD23 GSM1505750
221 GSM1505753_SMAD4_dMS_P.sga dMS - SMAD4 - Paired-end SMAD4 GSM1505753
222 GSM1505753_SMAD4_dMS_S.sga dMS - SMAD4 - Single-end SMAD4 GSM1505753
223 GSM1505761_SOX17_dMS_P.sga dMS - SOX17 - Paired-end SOX17 GSM1505761
224 GSM1505761_SOX17_dMS_S.sga dMS - SOX17 - Single-end SOX17 GSM1505761
225 GSM1505767_SOX2_dMS_P.sga dMS - SOX2 - Paired-end SOX2 GSM1505767
226 GSM1505776_SRF_dMS_P.sga dMS - SRF - Paired-end SRF GSM1505776
227 GSM1505788_TCF4_dMS_P.sga dMS - TCF4 - Paired-end TCF4 GSM1505788
228 GSM1505788_TCF4_dMS_S.sga dMS - TCF4 - Single-end TCF4 GSM1505788
229 GSM1505795_THAP11_dMS_P.sga dMS - THAP11 - Paired-end THAP11 GSM1505795
230 GSM1505800_TRIM28_dMS_P.sga dMS - TRIM28 - Paired-end TRIM28 GSM1505800
231 GSM1505783_T_dMS_P.sga dMS - T - Paired-end T GSM1505783
232 GSM1505784_T_dMS_P.sga dMS - T - Paired-end T GSM1505784
233 GSM1505783_T_dMS_S.sga dMS - T - Single-end T GSM1505783

Notes on samples nomenclature

Cell lines used:

Merge samples

None.

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit) with --split-3 option for paired-end reads and mapped to the genome using Bowtie. SAM files were then converted into bam using samtools and to bed using bamToBed (bedtools). SGA conversion was carried out using bed2sga (ChIP-seq).
Inportant note: according to the publication, all the samples should have been paired-end but fastq-dump did not always output the 2 files expected (one with the 5' end reads and the other with the 3' end) for all samples. Instead in some cases it only output one file and in others 3. In the first case the samples were treated as single-end, whereas in the second the samples were splitted in single-end and paired-end.

References

Genome browser viewable files