Song 16, ChIP-seq of abscisic acid-reponsive transcription factors.

Description

Genomc maps of several transcription factor (ABF1, ABF3, ABF4, ANAC032, ANAC102, AT5G04760, DREB2A, FBH3, GBF2, GBF3, HAT22, HB5, HB6, HB7, HSFA6A, MYB3, MYB44, NFYB2, NFYC2, RD26, ZAT6) in whole seedlings treated with abscisic acid (ABA) and ethanol (EtOH, control).

Source

Samples

From A. thaliana (Feb 2011 TAIR10/araTha1).

ChIP-seq data:

Filename Description Feature GEO-ID
1 ABF1_ABA.sga Seedling|ABF1|ABA|All ABF1 -
2 GSM2130865.sga Seedling|ABF1|ABA|rep1 ABF1 GSM2130865
3 GSM2130867.sga Seedling|ABF1|ABA|rep2 ABF1 GSM2130867
4 GSM2130869.sga Seedling|ABF1|ABA|rep3 ABF1 GSM2130869
5 ABF1_EtOH.sga Seedling|ABF1|EtOH|All ABF1 -
6 GSM2130866.sga Seedling|ABF1|EtOH|rep1 ABF1 GSM2130866
7 GSM2130868.sga Seedling|ABF1|EtOH|rep2 ABF1 GSM2130868
8 GSM2130870.sga Seedling|ABF1|EtOH|rep3 ABF1 GSM2130870
9 ABF3_ABA.sga Seedling|ABF3|ABA|All ABF3 -
10 GSM2130975.sga Seedling|ABF3|ABA|rep1 ABF3 GSM2130975
11 GSM2130977.sga Seedling|ABF3|ABA|rep2 ABF3 GSM2130977
12 GSM2130979.sga Seedling|ABF3|ABA|rep3 ABF3 GSM2130979
13 ABF3_EtOH.sga Seedling|ABF3|EtOH|All ABF3 -
14 GSM2130976.sga Seedling|ABF3|EtOH|rep1 ABF3 GSM2130976
15 GSM2130978.sga Seedling|ABF3|EtOH|rep2 ABF3 GSM2130978
16 GSM2130980.sga Seedling|ABF3|EtOH|rep3 ABF3 GSM2130980
17 ABF4_ABA.sga Seedling|ABF4|ABA|All ABF4 -
18 GSM2130969.sga Seedling|ABF4|ABA|rep1 ABF4 GSM2130969
19 GSM2130971.sga Seedling|ABF4|ABA|rep2 ABF4 GSM2130971
20 GSM2130973.sga Seedling|ABF4|ABA|rep3 ABF4 GSM2130973
21 ABF4_EtOH.sga Seedling|ABF4|EtOH|All ABF4 -
22 GSM2130970.sga Seedling|ABF4|EtOH|rep1 ABF4 GSM2130970
23 GSM2130972.sga Seedling|ABF4|EtOH|rep2 ABF4 GSM2130972
24 GSM2130974.sga Seedling|ABF4|EtOH|rep3 ABF4 GSM2130974
25 ANAC032_ABA.sga Seedling|ANAC032|ABA|All ANAC032 -
26 GSM2130881.sga Seedling|ANAC032|ABA|rep1 ANAC032 GSM2130881
27 GSM2130883.sga Seedling|ANAC032|ABA|rep2 ANAC032 GSM2130883
28 GSM2130885.sga Seedling|ANAC032|ABA|rep3 ANAC032 GSM2130885
29 ANAC032_EtOH.sga Seedling|ANAC032|EtOH|All ANAC032 -
30 GSM2130882.sga Seedling|ANAC032|EtOH|rep1 ANAC032 GSM2130882
31 GSM2130884.sga Seedling|ANAC032|EtOH|rep2 ANAC032 GSM2130884
32 GSM2130886.sga Seedling|ANAC032|EtOH|rep3 ANAC032 GSM2130886
33 ANAC102_ABA.sga Seedling|ANAC102|ABA|All ANAC102 -
34 GSM2130877.sga Seedling|ANAC102|ABA|rep1 ANAC102 GSM2130877
35 GSM2130879.sga Seedling|ANAC102|ABA|rep2 ANAC102 GSM2130879
36 ANAC102_EtOH.sga Seedling|ANAC102|EtOH|All ANAC102 -
37 GSM2130878.sga Seedling|ANAC102|EtOH|rep1 ANAC102 GSM2130878
38 GSM2130880.sga Seedling|ANAC102|EtOH|rep2 ANAC102 GSM2130880
39 AT5G04760_ABA.sga Seedling|AT5G04760|ABA|All AT5G04760 -
40 GSM2130957.sga Seedling|AT5G04760|ABA|rep1 AT5G04760 GSM2130957
41 GSM2130959.sga Seedling|AT5G04760|ABA|rep2 AT5G04760 GSM2130959
42 GSM2130961.sga Seedling|AT5G04760|ABA|rep3 AT5G04760 GSM2130961
43 AT5G04760_EtOH.sga Seedling|AT5G04760|EtOH|All AT5G04760 -
44 GSM2130958.sga Seedling|AT5G04760|EtOH|rep1 AT5G04760 GSM2130958
45 GSM2130960.sga Seedling|AT5G04760|EtOH|rep2 AT5G04760 GSM2130960
46 GSM2130962.sga Seedling|AT5G04760|EtOH|rep3 AT5G04760 GSM2130962
47 DREB2A_ABA.sga Seedling|DREB2A|ABA|All DREB2A -
48 GSM2130917.sga Seedling|DREB2A|ABA|rep1 DREB2A GSM2130917
49 GSM2130919.sga Seedling|DREB2A|ABA|rep2 DREB2A GSM2130919
50 GSM2130921.sga Seedling|DREB2A|ABA|rep3 DREB2A GSM2130921
51 DREB2A_EtOH.sga Seedling|DREB2A|EtOH|All DREB2A -
52 GSM2130918.sga Seedling|DREB2A|EtOH|rep1 DREB2A GSM2130918
53 GSM2130920.sga Seedling|DREB2A|EtOH|rep2 DREB2A GSM2130920
54 GSM2130922.sga Seedling|DREB2A|EtOH|rep3 DREB2A GSM2130922
55 FBH3_ABA.sga Seedling|FBH3|ABA|All FBH3 -
56 GSM2130905.sga Seedling|FBH3|ABA|rep1 FBH3 GSM2130905
57 GSM2130907.sga Seedling|FBH3|ABA|rep2 FBH3 GSM2130907
58 GSM2130909.sga Seedling|FBH3|ABA|rep3 FBH3 GSM2130909
59 FBH3_EtOH.sga Seedling|FBH3|EtOH|All FBH3 -
60 GSM2130906.sga Seedling|FBH3|EtOH|rep1 FBH3 GSM2130906
61 GSM2130908.sga Seedling|FBH3|EtOH|rep2 FBH3 GSM2130908
62 GSM2130910.sga Seedling|FBH3|EtOH|rep3 FBH3 GSM2130910
63 GBF2_ABA.sga Seedling|GBF2|ABA|All GBF2 -
64 GSM2130893.sga Seedling|GBF2|ABA|rep1 GBF2 GSM2130893
65 GSM2130895.sga Seedling|GBF2|ABA|rep2 GBF2 GSM2130895
66 GSM2130897.sga Seedling|GBF2|ABA|rep3 GBF2 GSM2130897
67 GBF2_EtOH.sga Seedling|GBF2|EtOH|All GBF2 -
68 GSM2130894.sga Seedling|GBF2|EtOH|rep1 GBF2 GSM2130894
69 GSM2130896.sga Seedling|GBF2|EtOH|rep2 GBF2 GSM2130896
70 GSM2130898.sga Seedling|GBF2|EtOH|rep3 GBF2 GSM2130898
71 GBF3_ABA.sga Seedling|GBF3|ABA|All GBF3 -
72 GSM2130871.sga Seedling|GBF3|ABA|rep1 GBF3 GSM2130871
73 GSM2130873.sga Seedling|GBF3|ABA|rep2 GBF3 GSM2130873
74 GSM2130875.sga Seedling|GBF3|ABA|rep3 GBF3 GSM2130875
75 GBF3_EtOH.sga Seedling|GBF3|EtOH|All GBF3 -
76 GSM2130872.sga Seedling|GBF3|EtOH|rep1 GBF3 GSM2130872
77 GSM2130874.sga Seedling|GBF3|EtOH|rep2 GBF3 GSM2130874
78 GSM2130876.sga Seedling|GBF3|EtOH|rep3 GBF3 GSM2130876
79 HAT22_ABA.sga Seedling|HAT22|ABA|All HAT22 -
80 GSM2130899.sga Seedling|HAT22|ABA|rep1 HAT22 GSM2130899
81 GSM2130901.sga Seedling|HAT22|ABA|rep2 HAT22 GSM2130901
82 GSM2130903.sga Seedling|HAT22|ABA|rep3 HAT22 GSM2130903
83 HAT22_EtOH.sga Seedling|HAT22|EtOH|All HAT22 -
84 GSM2130900.sga Seedling|HAT22|EtOH|rep1 HAT22 GSM2130900
85 GSM2130902.sga Seedling|HAT22|EtOH|rep2 HAT22 GSM2130902
86 GSM2130904.sga Seedling|HAT22|EtOH|rep3 HAT22 GSM2130904
87 HB5_ABA.sga Seedling|HB5|ABA|All HB5 -
88 GSM2130941.sga Seedling|HB5|ABA|rep1 HB5 GSM2130941
89 GSM2130943.sga Seedling|HB5|ABA|rep2 HB5 GSM2130943
90 GSM2130945.sga Seedling|HB5|ABA|rep3 HB5 GSM2130945
91 HB5_EtOH.sga Seedling|HB5|EtOH|All HB5 -
92 GSM2130942.sga Seedling|HB5|EtOH|rep1 HB5 GSM2130942
93 GSM2130944.sga Seedling|HB5|EtOH|rep2 HB5 GSM2130944
94 GSM2130946.sga Seedling|HB5|EtOH|rep3 HB5 GSM2130946
95 HB6_ABA.sga Seedling|HB6|ABA|All HB6 -
96 GSM2130947.sga Seedling|HB6|ABA|rep1 HB6 GSM2130947
97 GSM2130949.sga Seedling|HB6|ABA|rep2 HB6 GSM2130949
98 GSM2130951.sga Seedling|HB6|ABA|rep3 HB6 GSM2130951
99 HB6_EtOH.sga Seedling|HB6|EtOH|All HB6 -
100 GSM2130948.sga Seedling|HB6|EtOH|rep1 HB6 GSM2130948
101 GSM2130950.sga Seedling|HB6|EtOH|rep2 HB6 GSM2130950
102 GSM2130952.sga Seedling|HB6|EtOH|rep3 HB6 GSM2130952
103 HB7_ABA.sga Seedling|HB7|ABA|All HB7 -
104 GSM2130963.sga Seedling|HB7|ABA|rep1 HB7 GSM2130963
105 GSM2130965.sga Seedling|HB7|ABA|rep2 HB7 GSM2130965
106 GSM2130967.sga Seedling|HB7|ABA|rep3 HB7 GSM2130967
107 HB7_EtOH.sga Seedling|HB7|EtOH|All HB7 -
108 GSM2130964.sga Seedling|HB7|EtOH|rep1 HB7 GSM2130964
109 GSM2130966.sga Seedling|HB7|EtOH|rep2 HB7 GSM2130966
110 GSM2130968.sga Seedling|HB7|EtOH|rep3 HB7 GSM2130968
111 HSFA6A_ABA.sga Seedling|HSFA6A|ABA|All HSFA6A -
112 GSM2130929.sga Seedling|HSFA6A|ABA|rep1 HSFA6A GSM2130929
113 GSM2130931.sga Seedling|HSFA6A|ABA|rep2 HSFA6A GSM2130931
114 GSM2130933.sga Seedling|HSFA6A|ABA|rep3 HSFA6A GSM2130933
115 HSFA6A_EtOH.sga Seedling|HSFA6A|EtOH|All HSFA6A -
116 GSM2130930.sga Seedling|HSFA6A|EtOH|rep1 HSFA6A GSM2130930
117 GSM2130932.sga Seedling|HSFA6A|EtOH|rep2 HSFA6A GSM2130932
118 GSM2130934.sga Seedling|HSFA6A|EtOH|rep3 HSFA6A GSM2130934
119 MYB3_ABA.sga Seedling|MYB3|ABA|All MYB3 -
120 GSM2130911.sga Seedling|MYB3|ABA|rep1 MYB3 GSM2130911
121 GSM2130913.sga Seedling|MYB3|ABA|rep2 MYB3 GSM2130913
122 GSM2130915.sga Seedling|MYB3|ABA|rep3 MYB3 GSM2130915
123 MYB3_EtOH.sga Seedling|MYB3|EtOH|All MYB3 -
124 GSM2130912.sga Seedling|MYB3|EtOH|rep1 MYB3 GSM2130912
125 GSM2130914.sga Seedling|MYB3|EtOH|rep2 MYB3 GSM2130914
126 GSM2130916.sga Seedling|MYB3|EtOH|rep3 MYB3 GSM2130916
127 MYB44_ABA.sga Seedling|MYB44|ABA|All MYB44 -
128 GSM2130935.sga Seedling|MYB44|ABA|rep1 MYB44 GSM2130935
129 GSM2130937.sga Seedling|MYB44|ABA|rep2 MYB44 GSM2130937
130 GSM2130939.sga Seedling|MYB44|ABA|rep3 MYB44 GSM2130939
131 MYB44_EtOH.sga Seedling|MYB44|EtOH|All MYB44 -
132 GSM2130936.sga Seedling|MYB44|EtOH|rep1 MYB44 GSM2130936
133 GSM2130938.sga Seedling|MYB44|EtOH|rep2 MYB44 GSM2130938
134 GSM2130940.sga Seedling|MYB44|EtOH|rep3 MYB44 GSM2130940
135 NFYB2_ABA.sga Seedling|NFYB2|ABA|All NFYB2 -
136 GSM2130859.sga Seedling|NFYB2|ABA|rep1 NFYB2 GSM2130859
137 GSM2130861.sga Seedling|NFYB2|ABA|rep2 NFYB2 GSM2130861
138 GSM2130863.sga Seedling|NFYB2|ABA|rep3 NFYB2 GSM2130863
139 NFYB2_EtOH.sga Seedling|NFYB2|EtOH|All NFYB2 -
140 GSM2130860.sga Seedling|NFYB2|EtOH|rep1 NFYB2 GSM2130860
141 GSM2130862.sga Seedling|NFYB2|EtOH|rep2 NFYB2 GSM2130862
142 GSM2130864.sga Seedling|NFYB2|EtOH|rep3 NFYB2 GSM2130864
143 NFYC2_ABA.sga Seedling|NFYC2|ABA|All NFYC2 -
144 GSM2130887.sga Seedling|NFYC2|ABA|rep1 NFYC2 GSM2130887
145 GSM2130889.sga Seedling|NFYC2|ABA|rep2 NFYC2 GSM2130889
146 GSM2130891.sga Seedling|NFYC2|ABA|rep3 NFYC2 GSM2130891
147 NFYC2_EtOH.sga Seedling|NFYC2|EtOH|All NFYC2 -
148 GSM2130888.sga Seedling|NFYC2|EtOH|rep1 NFYC2 GSM2130888
149 GSM2130890.sga Seedling|NFYC2|EtOH|rep2 NFYC2 GSM2130890
150 GSM2130892.sga Seedling|NFYC2|EtOH|rep3 NFYC2 GSM2130892
151 RD26_ABA.sga Seedling|RD26|ABA|All RD26 -
152 GSM2130923.sga Seedling|RD26|ABA|rep1 RD26 GSM2130923
153 GSM2130925.sga Seedling|RD26|ABA|rep2 RD26 GSM2130925
154 GSM2130927.sga Seedling|RD26|ABA|rep3 RD26 GSM2130927
155 RD26_EtOH.sga Seedling|RD26|EtOH|All RD26 -
156 GSM2130924.sga Seedling|RD26|EtOH|rep1 RD26 GSM2130924
157 GSM2130926.sga Seedling|RD26|EtOH|rep2 RD26 GSM2130926
158 GSM2130928.sga Seedling|RD26|EtOH|rep3 RD26 GSM2130928
159 ZAT6_ABA.sga Seedling|ZAT6|ABA|All ZAT6 -
160 GSM2130953.sga Seedling|ZAT6|ABA|rep1 ZAT6 GSM2130953
161 GSM2130955.sga Seedling|ZAT6|ABA|rep2 ZAT6 GSM2130955
162 ZAT6_EtOH.sga Seedling|ZAT6|EtOH|All ZAT6 -
163 GSM2130954.sga Seedling|ZAT6|EtOH|rep1 ZAT6 GSM2130954
164 GSM2130956.sga Seedling|ZAT6|EtOH|rep2 ZAT6 GSM2130956
165 mockChIP_mock.sga Seedling|mockChIP|mock|All mockChIP -
166 GSM2130981.sga Seedling|Control|mock|rep1 mockChIP GSM2130981
167 GSM2130982.sga Seedling|Control|mock|rep2 mockChIP GSM2130982

Merged samples:

Replicas from the same TF and treatment have been merged and annotated as 'All'

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie2 v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).

References

Last update: 18 May 2017