Siersbaek 2020, ATAC-seq and ChIP-seq against ER, FOXA1, STAT3 and H3K27ac in IL6 treated cell lines and clinical samples.

ChIP-seq against transcription factors ER, FOXA1, STAT3 and the histone mark H3K27ac were applied to IL6 or vehicle treated T47D cells under FOXA1 knockdown and control conditions. In parallel, ATAC-seq assays were applied to the same samples.

ChIP-seq against ER, FOXA1 and STAT3 was also applied to IL-6 and vehicle treated MCF7 cells and two surgically resected primary ER+/pSTAT3+ breast tumors.

• Raw data was downloaded from SRA, bioproject: PRJNA518884
• Input file format: FASTQ
• Download date: 3-11-2021

From H. sapiens (Feb 2009 GRCh37/hg19).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	JC4726_ER_veh_T47D.sga	T47D|ESR1|veh|pas7	ESR1	GSM3587721
2	JC4727_ER_IL6_T47D.sga	T47D|ESR1|IL6|pas7	ESR1	GSM3587722
3	JC4728_ER_veh_T47D.sga	T47D|ESR1|veh|pas8	ESR1	GSM3587723
4	JC4729_ER_IL6_T47D.sga	T47D|ESR1|IL6|pas8	ESR1	GSM3587724
5	JC4730_ER_veh_T47D.sga	T47D|ESR1|veh|pas9	ESR1	GSM3587725
6	JC4731_ER_IL6_T47D.sga	T47D|ESR1|IL6|pas9	ESR1	GSM3587726
7	JC4732_ER_veh_T47D.sga	T47D|ESR1|veh|pas10	ESR1	GSM3587727
8	JC4733_ER_IL6_T47D.sga	T47D|ESR1|IL6|pas10	ESR1	GSM3587728
9	JC4734_STAT3_veh_T47D.sga	T47D|STAT3|veh|pas7	STAT3	GSM3587729
10	JC4735_STAT3_IL6_T47D.sga	T47D|STAT3|IL6|pas7	STAT3	GSM3587730
11	JC4736_STAT3_veh_T47D.sga	T47D|STAT3|veh|pas8	STAT3	GSM3587731
12	JC4737_STAT3_IL6_T47D.sga	T47D|STAT3|IL6|pas8	STAT3	GSM3587732
13	JC4738_STAT3_veh_T47D.sga	T47D|STAT3|veh|pas9	STAT3	GSM3587733
14	JC4739_STAT3_IL6_T47D.sga	T47D|STAT3|IL6|pas9	STAT3	GSM3587734
15	JC4740_STAT3_veh_T47D.sga	T47D|STAT3|veh|pas10	STAT3	GSM3587735
16	JC4741_STAT3_IL6_T47D.sga	T47D|STAT3|IL6|pas10	STAT3	GSM3587736
17	JC4742_FOXA1_veh_T47D.sga	T47D|FOXA1|veh|pas7	FOXA1	GSM3587737
18	JC4743_FOXA1_IL6_T47D.sga	T47D|FOXA1|IL6|pas7	FOXA1	GSM3587738
19	JC4744_FOXA1_veh_T47D.sga	T47D|FOXA1|veh|pas8	FOXA1	GSM3587739
20	JC4745_FOXA1_IL6_T47D.sga	T47D|FOXA1|IL6|pas8	FOXA1	GSM3587740
21	JC4746_FOXA1_veh_T47D.sga	T47D|FOXA1|veh|pas9	FOXA1	GSM3587741
22	JC4747_FOXA1_IL6_T47D.sga	T47D|FOXA1|IL6|pas9	FOXA1	GSM3587742
23	JC4748_FOXA1_veh_T47D.sga	T47D|FOXA1|veh|pas10	FOXA1	GSM3587743
24	JC4749_FOXA1_IL6_T47D.sga	T47D|FOXA1|IL6|pas10	FOXA1	GSM3587744
25	JC4750_pSTAT3_veh_T47D.sga	T47D|pSTAT3|veh|pas7	pSTAT3	GSM3587745
26	JC4751_pSTAT3_IL6_T47D.sga	T47D|pSTAT3|IL6|pas7	pSTAT3	GSM3587746
27	JC4752_pSTAT3_veh_T47D.sga	T47D|pSTAT3|veh|pas8	pSTAT3	GSM3587747
28	JC4753_pSTAT3_IL6_T47D.sga	T47D|pSTAT3|IL6|pas8	pSTAT3	GSM3587748
29	JC4754_pSTAT3_veh_T47D.sga	T47D|pSTAT3|veh|pas9	pSTAT3	GSM3587749
30	JC4755_pSTAT3_IL6_T47D.sga	T47D|pSTAT3|IL6|pas9	pSTAT3	GSM3587750
31	JC4756_pSTAT3_veh_T47D.sga	T47D|pSTAT3|veh|pas10	pSTAT3	GSM3587751
32	JC4757_pSTAT3_IL6_T47D.sga	T47D|pSTAT3|IL6|pas10	pSTAT3	GSM3587752
33	JC4782_Input_Veh_T47D.sga	T47D|Input|veh|pas7	Input	GSM3587753
34	JC4783_Input_Veh_T47D.sga	T47D|Input|veh|pas9	Input	GSM3587754
35	JC4784_Input_IL6_T47D.sga	T47D|Input|IL6|pas8	Input	GSM3587755
36	JC4785_Input_IL6_T47D.sga	T47D|Input|IL6|pas10	Input	GSM3587756
37	JC4690_FOXA1_Veh_MCF7.sga	MCF7|FOXA1|veh|pas31	FOXA1	GSM3587757
38	JC4691_FOXA1_IL6_MCF7.sga	MCF7|FOXA1|IL6|pas31	FOXA1	GSM3587758
39	JC4692_FOXA1_Veh_MCF7.sga	MCF7|FOXA1|veh|pas32	FOXA1	GSM3587759
40	JC4693_FOXA1_IL6_MCF7.sga	MCF7|FOXA1|IL6|pas32	FOXA1	GSM3587760
41	JC4694_FOXA1_Veh_MCF7.sga	MCF7|FOXA1|veh|pas33	FOXA1	GSM3587761
42	JC4695_FOXA1_IL6_MCF7.sga	MCF7|FOXA1|IL6|pas33	FOXA1	GSM3587762
43	JC4696_FOXA1_Veh_MCF7.sga	MCF7|FOXA1|veh|pas34	FOXA1	GSM3587763
44	JC4697_FOXA1_IL6_MCF7.sga	MCF7|FOXA1|IL6|pas34	FOXA1	GSM3587764
45	JC4722_Input_Veh_MCF7.sga	MCF7|Input|veh|pas30	Input	GSM3587765
46	JC4723_Input_Veh_MCF7.sga	MCF7|Input|veh|pas32	Input	GSM3587766
47	JC4724_Input_IL6_MCF7.sga	MCF7|Input|IL6|pas31	Input	GSM3587767
48	JC4725_Input_IL6_MCF7.sga	MCF7|Input|IL6|pas33	Input	GSM3587768
49	jc5833_pSTAT3_Veh_MCF7.sga	MCF7|pSTAT3|veh|pas22	pSTAT3	GSM3587769
50	jc5834_pSTAT3_IL6_MCF7.sga	MCF7|pSTAT3|IL6|pas22	pSTAT3	GSM3587770
51	jc5835_pSTAT3_Veh_MCF7.sga	MCF7|pSTAT3|veh|pas23	pSTAT3	GSM3587771
52	jc5836_pSTAT3_IL6_MCF7.sga	MCF7|pSTAT3|IL6|pas23	pSTAT3	GSM3587772
53	jc5837_pSTAT3_Veh_MCF7.sga	MCF7|pSTAT3|veh|pas24	pSTAT3	GSM3587773
54	jc5838_pSTAT3_IL6_MCF7.sga	MCF7|pSTAT3|IL6|pas24	pSTAT3	GSM3587774
55	jc5839_pSTAT3_Veh_MCF7.sga	MCF7|pSTAT3|veh|pas25	pSTAT3	GSM3587775
56	jc5840_pSTAT3_IL6_MCF7.sga	MCF7|pSTAT3|IL6|pas25	pSTAT3	GSM3587776
57	jc5841_STAT3_Veh_MCF7.sga	MCF7|STAT3|veh|pas22	STAT3	GSM3587777
58	jc5842_STAT3_IL6_MCF7.sga	MCF7|STAT3|IL6|pas22	STAT3	GSM3587778
59	jc5843_STAT3_Veh_MCF7.sga	MCF7|STAT3|veh|pas23	STAT3	GSM3587779
60	jc5844_STAT3_IL6_MCF7.sga	MCF7|STAT3|IL6|pas23	STAT3	GSM3587780
61	jc5845_STAT3_Veh_MCF7.sga	MCF7|STAT3|veh|pas24	STAT3	GSM3587781
62	jc5846_STAT3_IL6_MCF7.sga	MCF7|STAT3|IL6|pas24	STAT3	GSM3587782
63	jc5847_STAT3_Veh_MCF7.sga	MCF7|STAT3|veh|pas25	STAT3	GSM3587783
64	jc5848_STAT3_IL6_MCF7.sga	MCF7|STAT3|IL6|pas25	STAT3	GSM3587784
65	jc5849_ER_Veh_MCF7.sga	MCF7|ESR1|veh|pas22	ESR1	GSM3587785
66	jc5850_ER_IL6_MCF7.sga	MCF7|ESR1|IL6|pas22	ESR1	GSM3587786
67	jc5851_ER_Veh_MCF7.sga	MCF7|ESR1|veh|pas23	ESR1	GSM3587787
68	jc5852_ER_IL6_MCF7.sga	MCF7|ESR1|IL6|pas23	ESR1	GSM3587788
69	jc5853_ER_Veh_MCF7.sga	MCF7|ESR1|veh|pas24	ESR1	GSM3587789
70	jc5854_ER_IL6_MCF7.sga	MCF7|ESR1|IL6|pas24	ESR1	GSM3587790
71	jc5855_ER_Veh_MCF7.sga	MCF7|ESR1|veh|pas25	ESR1	GSM3587791
72	jc5856_ER_IL6_MCF7.sga	MCF7|ESR1|IL6|pas25	ESR1	GSM3587792
73	jc5857_Input_Veh_MCF7.sga	MCF7|Input|veh|pas22	Input	GSM3587793
74	jc5858_Input_IL6_MCF7.sga	MCF7|Input|IL6|pas22	Input	GSM3587794
75	jc5859_Input_Veh_MCF7.sga	MCF7|Input|veh|pas23	Input	GSM3587795
76	jc5860_Input_IL6_MCF7.sga	MCF7|Input|IL6|pas23	Input	GSM3587796
77	jc5861_Input_Veh_MCF7.sga	MCF7|Input|veh|pas24	Input	GSM3587797
78	jc5862_Input_IL6_MCF7.sga	MCF7|Input|IL6|pas24	Input	GSM3587798
79	jc5863_Input_Veh_MCF7.sga	MCF7|Input|veh|pas25	Input	GSM3587799
80	jc5864_Input_IL6_MCF7.sga	MCF7|Input|IL6|pas25	Input	GSM3587800
81	JC5053_pSTAT3_siCtl_PBS.sga	T47D|pSTAT3|siControl,PBS|pas25	pSTAT3	GSM3587801
82	JC5054_pSTAT3_siCtl_IL6.sga	T47D|pSTAT3|siControl,IL6|pas25	pSTAT3	GSM3587802
83	JC5055_pSTAT3_siFOXA1_PBS.sga	T47D|pSTAT3|siFOXA1,PBS|pas25	pSTAT3	GSM3587803
84	JC5056_pSTAT3_siFOXA1_IL6.sga	T47D|pSTAT3|siFOXA1,IL6|pas25	pSTAT3	GSM3587804
85	JC5057_pSTAT3_siCtl_PBS.sga	T47D|pSTAT3|siControl,PBS|pas26	pSTAT3	GSM3587805
86	JC5058_pSTAT3_siCtl_IL6.sga	T47D|pSTAT3|siControl,IL6|pas26	pSTAT3	GSM3587806
87	JC5059_pSTAT3_siFOXA1_PBS.sga	T47D|pSTAT3|siFOXA1,PBS|pas26	pSTAT3	GSM3587807
88	JC5060_pSTAT3_siFOXA1_IL6.sga	T47D|pSTAT3|siFOXA1,IL6|pas26	pSTAT3	GSM3587808
89	JC5061_pSTAT3_siCtl_PBS.sga	T47D|pSTAT3|siControl,PBS|pas27	pSTAT3	GSM3587809
90	JC5062_pSTAT3_siCtl_IL6.sga	T47D|pSTAT3|siControl,IL6|pas27	pSTAT3	GSM3587810
91	JC5063_pSTAT3_siFOXA1_PBS.sga	T47D|pSTAT3|siFOXA1,PBS|pas27	pSTAT3	GSM3587811
92	JC5064_pSTAT3_siFOXA1_IL6.sga	T47D|pSTAT3|siFOXA1,IL6|pas27	pSTAT3	GSM3587812
93	JC5065_pSTAT3_siCtl_PBS.sga	T47D|pSTAT3|siControl,PBS|pas29	pSTAT3	GSM3587813
94	JC5066_pSTAT3_siCtl_IL6.sga	T47D|pSTAT3|siControl,IL6|pas29	pSTAT3	GSM3587814
95	JC5067_pSTAT3_siFOXA1_PBS.sga	T47D|pSTAT3|siFOXA1,PBS|pas29	pSTAT3	GSM3587815
96	JC5068_pSTAT3_siFOXA1_IL6.sga	T47D|pSTAT3|siFOXA1,IL6|pas29	pSTAT3	GSM3587816
97	JC5069_H3K27ac_siCtl_PBS.sga	T47D|H3K27ac|siControl,PBS|pas25	H3K27ac	GSM3587817
98	JC5070_H3K27ac_siCtl_IL6.sga	T47D|H3K27ac|siControl,IL6|pas25	H3K27ac	GSM3587818
99	JC5071_H3K27ac_siFOXA1_PBS.sga	T47D|H3K27ac|siFOXA1,PBS|pas25	H3K27ac	GSM3587819
100	JC5072_H3K27ac_siFOXA1_IL6.sga	T47D|H3K27ac|siFOXA1,IL6|pas25	H3K27ac	GSM3587820
101	JC5073_H3K27ac_siCtl_PBS.sga	T47D|H3K27ac|siControl,PBS|pas26	H3K27ac	GSM3587821
102	JC5074_H3K27ac_siCtl_IL6.sga	T47D|H3K27ac|siControl,IL6|pas26	H3K27ac	GSM3587822
103	JC5075_H3K27ac_siFOXA1_PBS.sga	T47D|H3K27ac|siFOXA1,PBS|pas26	H3K27ac	GSM3587823
104	JC5076_H3K27ac_siFOXA1_IL6.sga	T47D|H3K27ac|siFOXA1,IL6|pas26	H3K27ac	GSM3587824
105	JC5077_H3K27ac_siCtl_PBS.sga	T47D|H3K27ac|siControl,PBS|pas27	H3K27ac	GSM3587825
106	JC5078_H3K27ac_siCtl_IL6.sga	T47D|H3K27ac|siControl,IL6|pas27	H3K27ac	GSM3587826
107	JC5079_H3K27ac_siFOXA1_PBS.sga	T47D|H3K27ac|siFOXA1,PBS|pas27	H3K27ac	GSM3587827
108	JC5080_H3K27ac_siFOXA1_IL6.sga	T47D|H3K27ac|siFOXA1,IL6|pas27	H3K27ac	GSM3587828
109	JC5081_H3K27ac_siCtl_PBS.sga	T47D|H3K27ac|siControl,PBS|pas29	H3K27ac	GSM3587829
110	JC5082_H3K27ac_siCtl_IL6.sga	T47D|H3K27ac|siControl,IL6|pas29	H3K27ac	GSM3587830
111	JC5083_H3K27ac_siFOXA1_PBS.sga	T47D|H3K27ac|siFOXA1,PBS|pas29	H3K27ac	GSM3587831
112	JC5084_H3K27ac_siFOXA1_IL6.sga	T47D|H3K27ac|siFOXA1,IL6|pas29	H3K27ac	GSM3587832
113	JC5085_Input_siCtl_PBS.sga	T47D|Input|siControl,PBS|pas25	Input	GSM3587833
114	JC5086_Input_siFOXA1_IL6.sga	T47D|Input|siFOXA1,IL6|pas25	Input	GSM3587834
115	JC5087_Input_siCtl_IL6.sga	T47D|Input|siControl,PBS|pas26	Input	GSM3587835
116	JC5088_Input_siFOXA1_PBS.sga	T47D|Input|siFOXA1,IL6|pas26	Input	GSM3587836
117	JC5089_Input_siCtl_PBS.sga	T47D|Input|siControl,PBS|pas27	Input	GSM3587837
118	JC5090_Input_siFOXA1_IL6.sga	T47D|Input|siFOXA1,IL6|pas27	Input	GSM3587838
119	JC5091_Input_siCtl_IL6.sga	T47D|Input|siControl,PBS|pas29	Input	GSM3587839
120	JC5092_Input_siFOXA1_PBS.sga	T47D|Input|siFOXA1,IL6|pas29	Input	GSM3587840
121	jc5554_pSTAT3_3840.sga	BT3840(ER+/pSTAT3+)|pSTAT3||	pSTAT3	GSM3587841
122	jc5555_pSTAT3_3487.sga	BT3487(ER+/pSTAT3+)|pSTAT3||	pSTAT3	GSM3587842
123	jc5572_ER_3840.sga	BT3840(ER+/pSTAT3+)|ESR1||	ESR1	GSM3587843
124	jc5573_ER_3487.sga	BT3487(ER+/pSTAT3+)|ESR1||	ESR1	GSM3587844
125	jc5583_FOXA1_3487.sga	BT3487(ER+/pSTAT3+)|FOXA1||	FOXA1	GSM3587845
126	jc5596_Input_3840.sga	BT3840(ER+/pSTAT3+)|Input||	Input	GSM3587846
127	jc5597_Input_3487.sga	BT3487(ER+/pSTAT3+)|Input||	Input	GSM3587847
128	T47D_ER_ChIP-seq_siCont_Veh_Input.sga	T47D|Input|siControl,veh|	Input	GSM4705573
129	T47D_ER_ChIP-seq_siCont_IL6_Input.sga	T47D|Input|siControl,IL6|	Input	GSM4705574
130	T47D_ER_ChIP-seq_siFOXA1_Veh_Input.sga	T47D|Input|siFOXA1,veh|	Input	GSM4705575
131	T47D_ER_ChIP-seq_siFOXA1_IL6_Input.sga	T47D|Input|siFOXA1,IL6|	Input	GSM4705576
132	T47D_ER_ChIP-seq_siCont_Veh_rep1.sga	T47D|ESR1|siControl,veh|rep1	ESR1	GSM4705577
133	T47D_ER_ChIP-seq_siCont_Veh_rep2.sga	T47D|ESR1|siControl,veh|rep2	ESR1	GSM4705578
134	T47D_ER_ChIP-seq_siCont_Veh_rep3.sga	T47D|ESR1|siControl,veh|rep3	ESR1	GSM4705579
135	T47D_ER_ChIP-seq_siCont_IL6_rep1.sga	T47D|ESR1|siControl,IL6|rep1	ESR1	GSM4705580
136	T47D_ER_ChIP-seq_siCont_IL6_rep2.sga	T47D|ESR1|siControl,IL6|rep2	ESR1	GSM4705581
137	T47D_ER_ChIP-seq_siCont_IL6_rep3.sga	T47D|ESR1|siControl,IL6|rep3	ESR1	GSM4705582
138	T47D_ER_ChIP-seq_siFOXA1_Veh_rep1.sga	T47D|ESR1|siFOXA1,veh|rep1	ESR1	GSM4705583
139	T47D_ER_ChIP-seq_siFOXA1_Veh_rep2.sga	T47D|ESR1|siFOXA1,veh|rep2	ESR1	GSM4705584
140	T47D_ER_ChIP-seq_siFOXA1_Veh_rep3.sga	T47D|ESR1|siFOXA1,veh|rep3	ESR1	GSM4705585
141	T47D_ER_ChIP-seq_siFOXA1_IL6_rep1.sga	T47D|ESR1|siFOXA1,IL6|rep1	ESR1	GSM4705586
142	T47D_ER_ChIP-seq_siFOXA1_IL6_rep2.sga	T47D|ESR1|siFOXA1,IL6|rep2	ESR1	GSM4705587
143	T47D_ER_ChIP-seq_siFOXA1_IL6_rep3.sga	T47D|ESR1|siFOXA1,IL6|rep3	ESR1	GSM4705588

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	jc6985_T47D_ATAC-seq_siCont_Veh.sga	T47D|ATAC-seq|siControl,Veh|pas27-30,rep1	ATACseq	GSM4524017
2	jc6986_T47D_ATAC-seq_siCont_IL6.sga	T47D|ATAC-seq|siControl,IL6|pas27-30,rep1	ATACseq	GSM4524018
3	jc6987_T47D_ATAC-seq_siFOXA1_Veh.sga	T47D|ATAC-seq|siFOXA1,Veh|pas27-30,rep1	ATACseq	GSM4524019
4	jc6988_T47D_ATAC-seq_siFOXA1_IL6.sga	T47D|ATAC-seq|siFOXA1,IL6|pas27-30,rep1	ATACseq	GSM4524020
5	jc6989_T47D_ATAC-seq_siCont_Veh.sga	T47D|ATAC-seq|siControl,Veh|pas27-30,rep2	ATACseq	GSM4524021
6	jc6990_T47D_ATAC-seq_siCont_IL6.sga	T47D|ATAC-seq|siControl,IL6|pas27-30,rep2	ATACseq	GSM4524022
7	jc6991_T47D_ATAC-seq_siFOXA1_Veh.sga	T47D|ATAC-seq|siFOXA1,Veh|pas27-30,rep2	ATACseq	GSM4524023
8	jc6992_T47D_ATAC-seq_siFOXA1_IL6.sga	T47D|ATAC-seq|siFOXA1,IL6|pas27-30,rep2	ATACseq	GSM4524024
9	jc6993_T47D_ATAC-seq_siCont_Veh.sga	T47D|ATAC-seq|siControl,Veh|pas27-30,rep3	ATACseq	GSM4524025
10	jc6994_T47D_ATAC-seq_siCont_IL6.sga	T47D|ATAC-seq|siControl,IL6|pas27-30.rep3	ATACseq	GSM4524026
11	jc6995_T47D_ATAC-seq_siFOXA1_Veh.sga	T47D|ATAC-seq|siFOXA1,Veh|pas27-30,rep3	ATACseq	GSM4524027
12	jc6996_T47D_ATAC-seq_siFOXA1_IL6.sga	T47D|ATAC-seq|siFOXA1,IL6|pas27-30,rep3	ATACseq	GSM4524028

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	merged_ER_IL6_MCF7.sga	MCF7|ESR1|IL6|all	ESR1	GSE126004
2	merged_ER_Veh_MCF7.sga	MCF7|ESR1|veh|all	ESR1	GSE126004
3	merged_FOXA1_IL6_MCF7.sga	MCF7|FOXA1|IL6|all	FOXA1	GSE126004
4	merged_FOXA1_Veh_MCF7.sga	MCF7|FOXA1|veh|all	FOXA1	GSE126004
5	merged_Input_IL6_MCF7.sga	MCF7|Input|IL6|all	Input	GSE126004
6	merged_Input_Veh_MCF7.sga	MCF7|Input|veh|all	Input	GSE126004
7	merged_STAT3_IL6_MCF7.sga	MCF7|STAT3|IL6|all	STAT3	GSE126004
8	merged_STAT3_Veh_MCF7.sga	MCF7|STAT3|veh|all	STAT3	GSE126004
9	merged_pSTAT3_IL6_MCF7.sga	MCF7|pSTAT3|IL6|all	pSTAT3	GSE126004
10	merged_pSTAT3_Veh_MCF7.sga	MCF7|pSTAT3|veh|all	pSTAT3	GSE126004
11	merged_ER_IL6_T47D.sga	T47D|ESR1|IL6|all	ESR1	GSE126004
12	merged_T47D_ER_ChIP-seq_siCont_IL6.sga	T47D|ESR1|siControl,IL6|all	ESR1	GSE126004
13	merged_T47D_ER_ChIP-seq_siCont_Veh.sga	T47D|ESR1|siControl,veh|all	ESR1	GSE126004
14	merged_T47D_ER_ChIP-seq_siFOXA1_IL6.sga	T47D|ESR1|siFOXA1,IL6|all	ESR1	GSE126004
15	merged_T47D_ER_ChIP-seq_siFOXA1_Veh.sga	T47D|ESR1|siFOXA1,veh|all	ESR1	GSE126004
16	merged_ER_veh_T47D.sga	T47D|ESR1|veh|all	ESR1	GSE126004
17	merged_FOXA1_IL6_T47D.sga	T47D|FOXA1|IL6|all	FOXA1	GSE126004
18	merged_FOXA1_veh_T47D.sga	T47D|FOXA1|veh|all	FOXA1	GSE126004
19	merged_H3K27ac_siCtl_IL6.sga	T47D|H3K27ac|siControl,IL6|all	H3K27ac	GSE126004
20	merged_H3K27ac_siCtl_PBS.sga	T47D|H3K27ac|siControl,PBS|all	H3K27ac	GSE126004
21	merged_H3K27ac_siFOXA1_IL6.sga	T47D|H3K27ac|siFOXA1,IL6|all	H3K27ac	GSE126004
22	merged_H3K27ac_siFOXA1_PBS.sga	T47D|H3K27ac|siFOXA1,PBS|all	H3K27ac	GSE126004
23	merged_Input_IL6_T47D.sga	T47D|Input|IL6|all	Input	GSE126004
24	merged_Input_siCtl_PBS.sga	T47D|Input|siControl,PBS|all	Input	GSE126004
25	merged_Input_siFOXA1_IL6.sga	T47D|Input|siFOXA1,IL6|all	Input	GSE126004
26	merged_Input_Veh_T47D.sga	T47D|Input|veh|all	Input	GSE126004
27	merged_STAT3_IL6_T47D.sga	T47D|STAT3|IL6|all	STAT3	GSE126004
28	merged_STAT3_veh_T47D.sga	T47D|STAT3|veh|all	STAT3	GSE126004
29	merged_pSTAT3_IL6_T47D.sga	T47D|pSTAT3|IL6|all	pSTAT3	GSE126004
30	merged_pSTAT3_siCtl_IL6.sga	T47D|pSTAT3|siControl,IL6|all	pSTAT3	GSE126004
31	merged_pSTAT3_siCtl_PBS.sga	T47D|pSTAT3|siControl,PBS|all	pSTAT3	GSE126004
32	merged_pSTAT3_siFOXA1_IL6.sga	T47D|pSTAT3|siFOXA1,IL6|all	pSTAT3	GSE126004
33	merged_pSTAT3_siFOXA1_PBS.sga	T47D|pSTAT3|siFOXA1,PBS|all	pSTAT3	GSE126004
34	merged_pSTAT3_veh_T47D.sga	T47D|pSTAT3|veh|all	pSTAT3	GSE126004

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	merged_T47D_ATAC-seq_siCont_Veh.sga	T47D|ATAC-seq|siControl,Veh|pas27-30,all	ATACseq	GSE126004
2	merged_T47D_ATAC-seq_siCont_IL6.sga	T47D|ATAC-seq|siControl,IL6|pas27-30,all	ATACseq	GSE126004
3	merged_T47D_ATAC-seq_siFOXA1_Veh.sga	T47D|ATAC-seq|siFOXA1,Veh|pas27-30,all	ATACseq	GSE126004
4	merged_T47D_ATAC-seq_siFOXA1_IL6.sga	T47D|ATAC-seq|siFOXA1,IL6|pas27-30,all	ATACseq	GSE126004

Notes on samples nomenclature:

BT3840 and BT3487 are two primary ER+ breast tumors.
pas7,8.. = passage 7,8..

Merged samples:

Data samples originating from the same type of experiment applied to different passages of the same cell cultures were merged. Samples designated as replicates of the same experiments were also merged. Merged SGA files are provided in addition to the component SGA files.

• Strand correlation plots: siersbaek20_strand_cor.pdf
• ChIP-seq tag enrichment around bound ESR1, FOXA1 or STAT3 motifs, respectively: siersbaek20_motif_enr.pdf

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v1.2.2. SAM files were then converted to BAM using samtools v1.9 and to BED using bamToBed v2.27.0 (bedtools). BED to SGA conversion was carried out using bed2sga (ChIP-Seq v. 1.5.5).

Note that ChIP-seq and ATAC-seq data are provided as single-end or paired-end reads, respectively, and were mapped to the genome with bowtie accordingly.

• Siersbaek R, Scabia V, Nagarajan S, Chernukhin I, Papachristou EK, Broome R, Johnston SJ, Joosten SEP, Green AR, Kumar S, Jones J, Omarjee S, Alvarez-Fernandez R, Glont S, Aitken SJ, Kishore K, Cheeseman D, Rakha EA, D'Santos C, Zwart W, Russell A, Brisken C, Carroll JS.
  IL6/STAT3 Signaling Hijacks Estrogen Receptor α Enhancers to Drive Breast Cancer Metastasis. Cancer Cell. 2020 Sep 14;38(3):412-423.e9. doi: 10.1016/j.ccell.2020.06.007. Epub 2020 Jul 16. PMID: 32679107
• GEO series GSE126006: IL6/STAT3 co-opts ER/FOXA1 regulatory elements to drive metastasis in breast cancer