Clouaire 2012, Cfp1 and H3k4me3 in ES cells

Description

ChIP-seq experiment of Cfp1 protein, various histone marks, RNA Pol II in several ES cells lines. Global Run-On of RNA of WT and Cfp1 -/- mutant cells. Cell lines used:
C169A: ES cell line expressing Cfp1, which has a missense mutation within the CxxC motif that abolishes DNA binding

Source

Files downloaded from ArrayExpress: E-ERAD-79, E-ERAD-80, E-ERAD-53.
Input file format: FASTQ

Samples

From Mouse Jul. 2007 (NCBI37/mm9) Assembly

Filename Description Feature GEO-ID
1 ERR156826.sga C169A|H3K4me1|rep 1 H3K4me1 -
2 ERR156827.sga C169A|H3K4me1|rep 2 H3K4me1 -
3 ERR156802.sga C169A|H3K4me3|rep 1 H3K4me3 -
4 ERR156803.sga C169A|H3K4me3|rep 2 H3K4me3 -
5 ERR156819.sga C169A|Pol2-4H8|rep 1 Pol2-4H8 -
6 ERR156820.sga C169A|Pol2-4H8|rep 2 Pol2-4H8 -
7 ERR156810.sga C169A|RNA Pol II|rep 1 Pol2 -
8 ERR156811.sga C169A|RNA Pol II|rep 2 Pol2 -
9 ERR156833.sga C169A|input_DNA|rep 1 input_DNA -
10 ERR156834.sga C169A|input_DNA|rep 2 input_DNA -
11 ERR156842.sga C169A|ubiquityl-H2B|rep 1 ubiquityl-H2B -
12 ERR156843.sga C169A|ubiquityl-H2B|rep 2 ubiquityl-H2B -
13 ERR156846.sga ES cells + C169A rescue|Cfp1|rep 1 Cfp1 -
14 ERR156844.sga ES cells + WT rescue|Cfp1|rep 1 Cfp1 -
15 ERR156845.sga ES cells + WT rescue|Cfp1|rep 2 Cfp1 -
16 ERR156783.sga ES cells|Cfp1|rep 1 Cfp1 -
17 ERR156784.sga ES cells|Cfp1|rep 2 Cfp1 -
18 ERR156785.sga ES cells|Cfp1|rep 3 Cfp1 -
19 ERR156786.sga ES cells|Cfp1|rep 4 Cfp1 -
20 ERR156788.sga ES cells|Cfp1|rep 5 Cfp1 -
21 ERR156789.sga ES cells|Cfp1|rep 6 Cfp1 -
22 ERR156790.sga ES cells|Cfp1|rep 7 Cfp1 -
23 ERR156791.sga ES cells|Cfp1|rep 8 Cfp1 -
24 ERR271293.sga ES cells|H3Ac|rep 1 H3Ac -
25 ERR271294.sga ES cells|H3Ac|rep 2 H3Ac -
26 ERR271295.sga ES cells|H3Ac|rep 3 H3Ac -
27 ERR271296.sga ES cells|H3Ac|rep 4 H3Ac -
28 ERR271301.sga ES cells|H3Ac|rep 5 H3Ac -
29 ERR271302.sga ES cells|H3Ac|rep 6 H3Ac -
30 ERR271303.sga ES cells|H3Ac|rep 7 H3Ac -
31 ERR271304.sga ES cells|H3Ac|rep 8 H3Ac -
32 ERR156780.sga ES cells|H3K27me3|rep 1 H3K27me3 -
33 ERR156787.sga ES cells|H3K27me3|rep 2 H3K27me3 -
34 ERR156794.sga ES cells|H3K27me3|rep 3 H3K27me3 -
35 ERR156795.sga ES cells|H3K27me3|rep 4 H3K27me3 -
36 ERR156776.sga ES cells|H3K4me1|rep 1 H3K4me1 -
37 ERR156777.sga ES cells|H3K4me1|rep 2 H3K4me1 -
38 ERR156781.sga ES cells|H3K4me1|rep 3 H3K4me1 -
39 ERR156782.sga ES cells|H3K4me1|rep 4 H3K4me1 -
40 ERR156814.sga ES cells|H3K4me1|rep 5 H3K4me1 -
41 ERR156821.sga ES cells|H3K4me1|rep 6 H3K4me1 -
42 ERR156726.sga ES cells|H3K4me3|rep 1 H3K4me3 -
43 ERR156727.sga ES cells|H3K4me3|rep 2 H3K4me3 -
44 ERR156778.sga ES cells|H3K4me3|rep 3 H3K4me3 -
45 ERR156779.sga ES cells|H3K4me3|rep 4 H3K4me3 -
46 ERR156796.sga ES cells|H3K4me3|rep 5 H3K4me3 -
47 ERR156797.sga ES cells|H3K4me3|rep 6 H3K4me3 -
48 ERR271299.sga ES cells|H3K4me3|rep 7 H3K4me3 -
49 ERR271300.sga ES cells|H3K4me3|rep 8 H3K4me3 -
50 ERR271305.sga ES cells|H3K4me3|rep 9 H3K4me3 -
51 ERR271306.sga ES cells|H3K4me3|rep 10 H3K4me3 -
52 ERR271307.sga ES cells|H3K4me3|rep 11 H3K4me3 -
53 ERR271308.sga ES cells|H3K4me3|rep 12 H3K4me3 -
54 ERR271309.sga ES cells|H3K4me3|rep 13 H3K4me3 -
55 ERR271310.sga ES cells|H3K4me3|rep 14 H3K4me3 -
56 ERR156792.sga ES cells|H3K4me3b|rep 1 H3K4me3b -
57 ERR156793.sga ES cells|H3K4me3b|rep 2 H3K4me3b -
58 ERR156812.sga ES cells|Pol2-4H8|rep 1 Pol2-4H8 -
59 ERR156813.sga ES cells|Pol2-4H8|rep 2 Pol2-4H8 -
60 ERR156724.sga ES cells|PolII|rep 1 PolII -
61 ERR156725.sga ES cells|PolII|rep 2 PolII -
62 ERR156804.sga ES cells|RNA Pol II|rep 1 Pol2 -
63 ERR156805.sga ES cells|RNA Pol II|rep 2 Pol2 -
64 ERR271297.sga ES cells|input|rep 1 input -
65 ERR271298.sga ES cells|input|rep 2 input -
66 ERR156828.sga ES cells|input_DNA|rep 1 input_DNA -
67 ERR156835.sga ES cells|input_DNA|rep 2 input_DNA -
68 ERR156836.sga ES cells|ubiquityl-H2B|rep 1 ubiquityl-H2B -
69 ERR156837.sga ES cells|ubiquityl-H2B|rep 2 ubiquityl-H2B -
70 ERR156822.sga EV2|H3K4me1|rep 1 H3K4me1 -
71 ERR156823.sga EV2|H3K4me1|rep 2 H3K4me1 -
72 ERR156798.sga EV2|H3K4me3|rep 1 H3K4me3 -
73 ERR156799.sga EV2|H3K4me3|rep 2 H3K4me3 -
74 ERR156815.sga EV2|Pol2-4H8|rep 1 Pol2-4H8 -
75 ERR156816.sga EV2|Pol2-4H8|rep 2 Pol2-4H8 -
76 ERR156806.sga EV2|RNA Pol II|rep 1 Pol2 -
77 ERR156807.sga EV2|RNA Pol II|rep 2 Pol2 -
78 ERR156829.sga EV2|input_DNA|rep 1 input_DNA -
79 ERR156830.sga EV2|input_DNA|rep 2 input_DNA -
80 ERR156838.sga EV2|ubiquityl-H2B|rep 1 ubiquityl-H2B -
81 ERR156839.sga EV2|ubiquityl-H2B|rep 2 ubiquityl-H2B -
82 ERR411486.sga brain|Cfp1|rep 1 Cfp1 -
83 ERR411487.sga brain|Cfp1|rep 2 Cfp1 -
84 ERR411488.sga brain|Cfp1|rep 3 Cfp1 -
85 ERR411489.sga brain|Cfp1|rep 4 Cfp1 -
86 ERR411490.sga brain|Cfp1|rep 5 Cfp1 -
87 ERR411491.sga brain|Cfp1|rep 6 Cfp1 -
88 ERR411492.sga brain|Cfp1|rep 7 Cfp1 -
89 ERR411485.sga brain|H3K4me3|rep 1 H3K4me3 -
90 ERR156771.sga dendritic cells|H3Ac|rep 1 H3Ac -
91 ERR156772.sga dendritic cells|H3Ac|rep 2 H3Ac -
92 ERR156774.sga dendritic cells|H3Ac|rep 3 H3Ac -
93 ERR156775.sga dendritic cells|H3Ac|rep 4 H3Ac -
94 ERR156770.sga dendritic cells|input|rep 1 input -
95 ERR156773.sga dendritic cells|input|rep 2 input -
96 ERR156860.sga kd3T3|Cfp1|rep 1 Cfp1 -
97 ERR156858.sga kd3T3|H3K4me3|rep 1 H3K4me3 -
98 ERR156856.sga kd3T3|RNA Pol II|rep 1 Pol2 -
99 ERR156824.sga not specified|H3K4me1|rep 1 H3K4me1 -
100 ERR156825.sga not specified|H3K4me1|rep 2 H3K4me1 -
101 ERR156800.sga not specified|H3K4me3|rep 1 H3K4me3 -
102 ERR156801.sga not specified|H3K4me3|rep 2 H3K4me3 -
103 ERR156817.sga not specified|Pol2-4H8|rep 1 Pol2-4H8 -
104 ERR156818.sga not specified|Pol2-4H8|rep 2 Pol2-4H8 -
105 ERR156808.sga not specified|RNA Pol II|rep 1 Pol2 -
106 ERR156809.sga not specified|RNA Pol II|rep 2 Pol2 -
107 ERR156831.sga not specified|input_DNA|rep 1 input_DNA -
108 ERR156832.sga not specified|input_DNA|rep 2 input_DNA -
109 ERR156840.sga not specified|ubiquityl-H2B|rep 1 ubiquityl-H2B -
110 ERR156841.sga not specified|ubiquityl-H2B|rep 2 ubiquityl-H2B -
111 ERR156859.sga wt3T3|Cfp1|rep 1 Cfp1 -
112 ERR156857.sga wt3T3|H3K4me3|rep 1 H3K4me3 -
113 ERR156855.sga wt3T3|RNA Pol II|rep 1 Pol2 -
114 ERR156853.sga C169A|GRO|rep 1 Br-dUTP -
115 ERR156854.sga C169A|GRO|rep 2 Br-dUTP -
116 ERR156867.sga C169A|GRO|rep 3 Br-dUTP -
117 ERR156868.sga C169A|GRO|rep 4 Br-dUTP -
118 ERR156871.sga C169A|GRO|rep 5 Br-dUTP -
119 ERR156872.sga C169A|GRO|rep 6 Br-dUTP -
120 ERR156873.sga C169A|GRO|rep 7 Br-dUTP -
121 ERR156874.sga C169A|GRO|rep 8 Br-dUTP -
122 ERR156849.sga EV2|GRO|rep 1 Br-dUTP -
123 ERR156850.sga EV2|GRO|rep 2 Br-dUTP -
124 ERR156863.sga EV2|GRO|rep 3 Br-dUTP -
125 ERR156864.sga EV2|GRO|rep 4 Br-dUTP -
126 ERR156879.sga KO kainate|GRO|rep 1 Br-dUTP -
127 ERR156885.sga KO kainate|GRO|rep 2 Br-dUTP -
128 ERR156886.sga KO kainate|GRO|rep 3 Br-dUTP -
129 ERR156878.sga KO saline|GRO|rep 1 Br-dUTP -
130 ERR156883.sga KO saline|GRO|rep 2 Br-dUTP -
131 ERR156884.sga KO saline|GRO|rep 3 Br-dUTP -
132 ERR156847.sga wild type ES|GRO|rep 1 Br-dUTP -
133 ERR156848.sga wild type ES|GRO|rep 2 Br-dUTP -
134 ERR156861.sga wild type ES|GRO|rep 3 Br-dUTP -
135 ERR156862.sga wild type ES|GRO|rep 4 Br-dUTP -
136 ERR156870.sga wild type kainate|GRO|rep 1 Br-dUTP -
137 ERR156875.sga wild type kainate|GRO|rep 2 Br-dUTP -
138 ERR156876.sga wild type kainate|GRO|rep 3 Br-dUTP -
139 ERR156877.sga wild type kainate|GRO|rep 4 Br-dUTP -
140 ERR156851.sga wild type rescue|GRO|rep 1 Br-dUTP -
141 ERR156852.sga wild type rescue|GRO|rep 2 Br-dUTP -
142 ERR156865.sga wild type rescue|GRO|rep 3 Br-dUTP -
143 ERR156866.sga wild type rescue|GRO|rep 4 Br-dUTP -
144 ERR156869.sga wild type saline|GRO|rep 1 Br-dUTP -
145 ERR156880.sga wild type saline|GRO|rep 2 Br-dUTP -
146 ERR156881.sga wild type saline|GRO|rep 3 Br-dUTP -
147 ERR156882.sga wild type saline|GRO|rep 4 Br-dUTP -

Technical Notes

FASTQ files were downloaded from ArrayExpress and mapped to the mouse genome (mm9) using bowtie.

References

  1. Clouaire T, Webb S, Skene P, Illingworth R, Kerr A, Andrews R, Lee JH, Skalnik D, Bird A.
    Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells. Genes Dev. 2012 Aug 1;26(15):1714-28. PMID: 22855832

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