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