Garber 2012, Time course of 29 TFs and chromatin marks in primary dendritic cells

Description

Data downloaded from GEO series GSE36099: Genome-wide binding maps for 29 transcription factors (TFs) and chromatin marks at four time points following stimulation of primary dendritic cells (DCs) with pathogen components.

Source

Files downloaded from FTP site: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP011/SRP011071
Input file format: SRA

Samples

From Mouse Jul. 2007 (NCBI37/mm9) Assembly

Filename Description Feature GEO-ID
1 GSM881048_Ahr_0-min.sga Ahr 0-min post LPS stimulation Ahr GSM881048
2 GSM881050_Ahr_30-min.sga Ahr 30-min post LPS stimulation Ahr GSM881050
3 GSM881051_Ahr_60-min.sga Ahr 60-min post LPS stimulation Ahr GSM881051
4 GSM881049_Ahr_120-min.sga Ahr 120-min post LPS stimulation Ahr GSM881049
5 GSM881126_Atf3_0-min.sga Atf3 0-min post LPS stimulation Atf3 GSM881126
6 GSM881128_Atf3_30-min.sga Atf3 30-min post LPS stimulation Atf3 GSM881128
7 GSM881129_Atf3_60-min.sga Atf3 60-min post LPS stimulation Atf3 GSM881129
8 GSM881127_Atf3_120-min.sga Atf3 120-min post LPS stimulation Atf3 GSM881127
9 GSM881130_Atf4_120-min.sga Atf4 120-min post LPS stimulation Atf4 GSM881130
10 GSM881135_Cebpb_0-min.sga Cebpb 0-min post LPS stimulation Cebpb GSM881135
11 GSM881137_Cebpb_30-min.sga Cebpb 30-min post LPS stimulation Cebpb GSM881137
12 GSM881138_Cebpb_60-min.sga Cebpb 60-min post LPS stimulation Cebpb GSM881138
13 GSM881136_Cebpb_120-min.sga Cebpb 120-min post LPS stimulation Cebpb GSM881136
14 GSM881052_Ctcf_0-min.sga Ctcf 0-min post LPS stimulation Ctcf GSM881052
15 GSM881054_Ctcf_30-min.sga Ctcf 30-min post LPS stimulation Ctcf GSM881054
16 GSM881055_Ctcf_60-min.sga Ctcf 60-min post LPS stimulation Ctcf GSM881055
17 GSM881053_Ctcf_120-min.sga Ctcf 120-min post LPS stimulation Ctcf GSM881053
18 GSM881056_E2f1_0-min.sga E2f1 0-min post LPS stimulation E2f1 GSM881056
19 GSM881058_E2f1_30-min.sga E2f1 30-min post LPS stimulation E2f1 GSM881058
20 GSM881059_E2f1_60-min.sga E2f1 60-min post LPS stimulation E2f1 GSM881059
21 GSM881057_E2f1_120-min.sga E2f1 120-min post LPS stimulation E2f1 GSM881057
22 GSM881060_E2f4_0-min.sga E2f4 0-min post LPS stimulation E2f4 GSM881060
23 GSM881062_E2f4_30-min.sga E2f4 30-min post LPS stimulation E2f4 GSM881062
24 GSM881063_E2f4_60-min.sga E2f4 60-min post LPS stimulation E2f4 GSM881063
25 GSM881061_E2f4_120-min.sga E2f4 120-min post LPS stimulation E2f4 GSM881061
26 GSM881139_Egr1_0-min.sga Egr1 0-min post LPS stimulation Egr1 GSM881139
27 GSM881141_Egr1_30-min.sga Egr1 30-min post LPS stimulation Egr1 GSM881141
28 GSM881142_Egr1_60-min.sga Egr1 60-min post LPS stimulation Egr1 GSM881142
29 GSM881140_Egr1_120-min.sga Egr1 120-min post LPS stimulation Egr1 GSM881140
30 GSM881091_Egr2_0-min.sga Egr2 0-min post LPS stimulation Egr2 GSM881091
31 GSM881093_Egr2_30-min.sga Egr2 30-min post LPS stimulation Egr2 GSM881093
32 GSM881094_Egr2_60-min.sga Egr2 60-min post LPS stimulation Egr2 GSM881094
33 GSM881092_Egr2_120-min.sga Egr2 120-min post LPS stimulation Egr2 GSM881092
34 GSM881064_Ets2_0-min.sga Ets2 0-min post LPS stimulation Ets2 GSM881064
35 GSM881066_Ets2_30-min.sga Ets2 30-min post LPS stimulation Ets2 GSM881066
36 GSM881067_Ets2_60-min.sga Ets2 60-min post LPS stimulation Ets2 GSM881067
37 GSM881065_Ets2_120-min.sga Ets2 120-min post LPS stimulation Ets2 GSM881065
38 GSM881068_Hif1a_0-min.sga Hif1a 0-min post LPS stimulation Hif1a GSM881068
39 GSM881070_Hif1a_30-min.sga Hif1a 30-min post LPS stimulation Hif1a GSM881070
40 GSM881071_Hif1a_60-min.sga Hif1a 60-min post LPS stimulation Hif1a GSM881071
41 GSM881069_Hif1a_120-min.sga Hif1a 120-min post LPS stimulation Hif1a GSM881069
42 GSM881072_Irf1_0-min.sga Irf1 0-min post LPS stimulation Irf1 GSM881072
43 GSM881074_Irf1_30-min.sga Irf1 30-min post LPS stimulation Irf1 GSM881074
44 GSM881075_Irf1_60-min.sga Irf1 60-min post LPS stimulation Irf1 GSM881075
45 GSM881073_Irf1_120-min.sga Irf1 120-min post LPS stimulation Irf1 GSM881073
46 GSM881143_Irf2_0-min.sga Irf2 0-min post LPS stimulation Irf2 GSM881143
47 GSM881145_Irf2_30-min.sga Irf2 30-min post LPS stimulation Irf2 GSM881145
48 GSM881146_Irf2_60-min.sga Irf2 60-min post LPS stimulation Irf2 GSM881146
49 GSM881144_Irf2_120-min.sga Irf2 120-min post LPS stimulation Irf2 GSM881144
50 GSM881147_Irf4_0-min.sga Irf4 0-min post LPS stimulation Irf4 GSM881147
51 GSM881149_Irf4_30-min.sga Irf4 30-min post LPS stimulation Irf4 GSM881149
52 GSM881150_Irf4_60-min.sga Irf4 60-min post LPS stimulation Irf4 GSM881150
53 GSM881148_Irf4_120-min.sga Irf4 120-min post LPS stimulation Irf4 GSM881148
54 GSM881076_Junb_0-min.sga Junb 0-min post LPS stimulation Junb GSM881076
55 GSM881078_Junb_30-min.sga Junb 30-min post LPS stimulation Junb GSM881078
56 GSM881079_Junb_60-min.sga Junb 60-min post LPS stimulation Junb GSM881079
57 GSM881077_Junb_120-min.sga Junb 120-min post LPS stimulation Junb GSM881077
58 GSM881080_K27Ac_0-min.sga K27Ac 0-min post LPS stimulation K27Ac GSM881080
59 GSM881082_K27Ac_30-min.sga K27Ac 30-min post LPS stimulation K27Ac GSM881082
60 GSM881083_K27Ac_60-min.sga K27Ac 60-min post LPS stimulation K27Ac GSM881083
61 GSM881081_K27Ac_120-min.sga K27Ac 120-min post LPS stimulation K27Ac GSM881081
62 GSM881084_K4me1_0-min.sga K4me1 0-min post LPS stimulation K4me1 GSM881084
63 GSM881085_K4me1_120-min.sga K4me1 120-min post LPS stimulation K4me1 GSM881085
64 GSM881086_K4me1_240-min.sga K4me1 240-min post LPS stimulation K4me1 GSM881086
65 GSM881087_K4me3_0-min.sga K4me3 0-min post LPS stimulation K4me3 GSM881087
66 GSM881089_K4me3_30-min.sga K4me3 30-min post LPS stimulation K4me3 GSM881089
67 GSM881090_K4me3_60-min.sga K4me3 60-min post LPS stimulation K4me3 GSM881090
68 GSM881088_K4me3_120-min.sga K4me3 120-min post LPS stimulation K4me3 GSM881088
69 GSM881095_Maff_0-min.sga Maff 0-min post LPS stimulation Maff GSM881095
70 GSM881097_Maff_30-min.sga Maff 30-min post LPS stimulation Maff GSM881097
71 GSM881098_Maff_60-min.sga Maff 60-min post LPS stimulation Maff GSM881098
72 GSM881096_Maff_120-min.sga Maff 120-min post LPS stimulation Maff GSM881096
73 GSM881151_Nfkb1_0-min.sga Nfkb1 0-min post LPS stimulation Nfkb1 GSM881151
74 GSM881153_Nfkb1_30-min.sga Nfkb1 30-min post LPS stimulation Nfkb1 GSM881153
75 GSM881154_Nfkb1_60-min.sga Nfkb1 60-min post LPS stimulation Nfkb1 GSM881154
76 GSM881152_Nfkb1_120-min.sga Nfkb1 120-min post LPS stimulation Nfkb1 GSM881152
77 GSM881099_PU1_0-min.sga PU1 0-min post LPS stimulation PU1 GSM881099
78 GSM881101_PU1_30-min.sga PU1 30-min post LPS stimulation PU1 GSM881101
79 GSM881102_PU1_60-min.sga PU1 60-min post LPS stimulation PU1 GSM881102
80 GSM881100_PU1_120-min.sga PU1 120-min post LPS stimulation PU1 GSM881100
81 GSM881103_Pol-II_0-min.sga Pol-II 0-min post LPS stimulation Pol-II GSM881103
82 GSM881104_Pol-II_15-min.sga Pol-II 15-min post LPS stimulation Pol-II GSM881104
83 GSM881105_Pol-II_30-min.sga Pol-II 30-min post LPS stimulation Pol-II GSM881105
84 GSM881106_Pol-II_60-min.sga Pol-II 60-min post LPS stimulation Pol-II GSM881106
85 GSM881131_Rel_0-min.sga Rel 0-min post LPS stimulation Rel GSM881131
86 GSM881133_Rel_30-min.sga Rel 30-min post LPS stimulation Rel GSM881133
87 GSM881134_Rel_60-min.sga Rel 60-min post LPS stimulation Rel GSM881134
88 GSM881132_Rel_120-min.sga Rel 120-min post LPS stimulation Rel GSM881132
89 GSM881163_Rel_120-min.sga Rel 120-min post LPS stimulation Rel GSM881163
90 GSM881111_Rela_0-min.sga Rela 0-min post LPS stimulation Rela GSM881111
91 GSM881113_Rela_30-min.sga Rela 30-min post LPS stimulation Rela GSM881113
92 GSM881114_Rela_60-min.sga Rela 60-min post LPS stimulation Rela GSM881114
93 GSM881112_Rela_120-min.sga Rela 120-min post LPS stimulation Rela GSM881112
94 GSM881107_Relb_0-min.sga Relb 0-min post LPS stimulation Relb GSM881107
95 GSM881109_Relb_30-min.sga Relb 30-min post LPS stimulation Relb GSM881109
96 GSM881110_Relb_60-min.sga Relb 60-min post LPS stimulation Relb GSM881110
97 GSM881108_Relb_120-min.sga Relb 120-min post LPS stimulation Relb GSM881108
98 GSM881164_Relb_120-min.sga Relb 120-min post LPS stimulation Relb GSM881164
99 GSM881115_Runx1_0-min.sga Runx1 0-min post LPS stimulation Runx1 GSM881115
100 GSM881117_Runx1_60-min.sga Runx1 60-min post LPS stimulation Runx1 GSM881117
101 GSM881116_Runx1_120-min.sga Runx1 120-min post LPS stimulation Runx1 GSM881116
102 GSM881155_Stat1_0-min.sga Stat1 0-min post LPS stimulation Stat1 GSM881155
103 GSM881157_Stat1_30-min.sga Stat1 30-min post LPS stimulation Stat1 GSM881157
104 GSM881158_Stat1_60-min.sga Stat1 60-min post LPS stimulation Stat1 GSM881158
105 GSM881156_Stat1_120-min.sga Stat1 120-min post LPS stimulation Stat1 GSM881156
106 GSM881159_Stat2_0-min.sga Stat2 0-min post LPS stimulation Stat2 GSM881159
107 GSM881161_Stat2_30-min.sga Stat2 30-min post LPS stimulation Stat2 GSM881161
108 GSM881162_Stat2_60-min.sga Stat2 60-min post LPS stimulation Stat2 GSM881162
109 GSM881160_Stat2_120-min.sga Stat2 120-min post LPS stimulation Stat2 GSM881160
110 GSM881118_Stat3_0-min.sga Stat3 0-min post LPS stimulation Stat3 GSM881118
111 GSM881120_Stat3_30-min.sga Stat3 30-min post LPS stimulation Stat3 GSM881120
112 GSM881121_Stat3_60-min.sga Stat3 60-min post LPS stimulation Stat3 GSM881121
113 GSM881119_Stat3_120-min.sga Stat3 120-min post LPS stimulation Stat3 GSM881119
114 GSM881122_WCE_0-min.sga WCE 0-min post LPS stimulation WCE GSM881122
115 GSM881124_WCE_30-min.sga WCE 30-min post LPS stimulation WCE GSM881124
116 GSM881125_WCE_60-min.sga WCE 60-min post LPS stimulation WCE GSM881125
117 GSM881123_WCE_120-min.sga WCE 120-min post LPS stimulation WCE GSM881123

Technical Notes

FASTQ files were generated from the SRA files downloared from the NCBI SRA repository. Sequence tags were mapped to mouse genome assembly Feb 2007 (NCBI37/mm9) using Bowtie. Please note that some of the samples have pared-ends and read lenghts are not constant.

References

  1. Garber M, Yosef N, Raychowdhury R, Thielke A, Bernstein B, Nusbaum C, Hacohen N, Regev A, Amit I
    A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell 2012 Sep 14; 47(5): 810-822. PMID: 22940246

  2. GEO series GSE36099 A high throughput in vivo protein-DNA mapping approach reveals principles of dynamic gene regulation in mammals (ChIP-Seq).

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