Takaku 2018, GATA3 zinc finger 2 mutations reprogram the breast cancer transcriptional network.

ChIP-seq data against GATA3 and GATA3 with mutations in the second GATA3 zinc-finger (ZnFn2) in breast cancer cell lines (T47D and CR3 mutant cells).

• Raw data was downloaded from: GSE99479
• Input file format: SRA
• Download date: 17-7-2019

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

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	ATACseq_CR3flp.oriented.sga	CR3flp|ATACseq|all	ATACseq	GSM2644565, GSM2644566, GSM2644567
2	ATACseq_CR3flp_long.centered.sga	CR3flp|ATACseq|long	ATACseq	GSM2644565, GSM2644566, GSM2644567
4	ATACseq_T47Dflp.oriented.sga	T47Dflp|ATACseq|all	ATACseq	GSM2644565, GSM2644566, GSM2644567
5	ATACseq_T47Dflp_long.centered.sga	T47Dflp|ATACseq|long	ATACseq	GSM2644561, GSM2644562, GSM2644563

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM2644567.centered.sga	T47Dflp|ESR1|None|rep1	ESR1	GSM2644567
2	GSM2644567.sga	T47Dflp|ESR1|None|rep1	ESR1	GSM2644567
3	GSM2644568.centered.sga	T47Dflp|ESR1|None|rep2	ESR1	GSM2644568
4	GSM2644568.sga	T47Dflp|ESR1|None|rep2	ESR1	GSM2644568
5	GSM2644569.centered.sga	CR3flp|ESR1|None|rep1	ESR1	GSM2644569
6	GSM2644569.sga	CR3flp|ESR1|None|rep1	ESR1	GSM2644569
7	GSM2644570.centered.sga	CR3flp|ESR1|None|rep2	ESR1	GSM2644570
8	GSM2644570.sga	CR3flp|ESR1|None|rep2	ESR1	GSM2644570
9	GSM2644571.centered.sga	T47Dflp|N-GATA3|None|rep1	N-GATA3	GSM2644571
10	GSM2644571.sga	T47Dflp|N-GATA3|None|rep1	N-GATA3	GSM2644571
11	GSM2644572.centered.sga	T47Dflp|N-GATA3|None|rep2	N-GATA3	GSM2644572
12	GSM2644572.sga	T47Dflp|N-GATA3|None|rep2	N-GATA3	GSM2644572
13	GSM2644573.centered.sga	CR3flp|N-GATA3|None|rep1	N-GATA3	GSM2644573
14	GSM2644573.sga	CR3flp|N-GATA3|None|rep1	N-GATA3	GSM2644573
15	GSM2644574.centered.sga	CR3flp|N-GATA3|None|rep2	N-GATA3	GSM2644574
16	GSM2644574.sga	CR3flp|N-GATA3|None|rep2	N-GATA3	GSM2644574
17	GSM2644575.centered.sga	T47Dflp|FOXA1|None|rep1	FOXA1	GSM2644575
18	GSM2644575.sga	T47Dflp|FOXA1|None|rep1	FOXA1	GSM2644575
19	GSM2644576.centered.sga	T47Dflp|FOXA1|None|rep2	FOXA1	GSM2644576
20	GSM2644576.sga	T47Dflp|FOXA1|None|rep2	FOXA1	GSM2644576
21	GSM2644577.centered.sga	CR3flp|FOXA1|None|rep1	FOXA1	GSM2644577
22	GSM2644577.sga	CR3flp|FOXA1|None|rep1	FOXA1	GSM2644577
23	GSM2644578.centered.sga	CR3flp|FOXA1|None|rep2	FOXA1	GSM2644578
24	GSM2644578.sga	CR3flp|FOXA1|None|rep2	FOXA1	GSM2644578
25	GSM2644579.centered.sga	T47Dflp|C-GATA3|None|rep1	C-GATA3	GSM2644579
26	GSM2644579.sga	T47Dflp|C-GATA3|None|rep1	C-GATA3	GSM2644579
27	GSM2644580.centered.sga	T47Dflp|C-GATA3|None|rep2	C-GATA3	GSM2644580
28	GSM2644580.sga	T47Dflp|C-GATA3|None|rep2	C-GATA3	GSM2644580
29	GSM2644581.centered.sga	CR3flp|C-GATA3|None|rep1	C-GATA3	GSM2644581
30	GSM2644581.sga	CR3flp|C-GATA3|None|rep1	C-GATA3	GSM2644581
31	GSM2644582.centered.sga	CR3flp|C-GATA3|None|rep2	C-GATA3	GSM2644582
32	GSM2644582.sga	CR3flp|C-GATA3|None|rep2	C-GATA3	GSM2644582
33	GSM2644583.centered.sga	T47Dflp|input|None|rep1	input	GSM2644583
34	GSM2644583.sga	T47Dflp|input|None|rep1	input	GSM2644583
35	GSM2644584.centered.sga	T47Dflp|input|None|rep2	input	GSM2644584
36	GSM2644584.sga	T47Dflp|input|None|rep2	input	GSM2644584
37	GSM2644585.centered.sga	CR3|input|None|rep1	input	GSM2644585
38	GSM2644585.sga	CR3|input|None|rep1	input	GSM2644585
39	GSM2644586.centered.sga	CR3|input|None|rep2	input	GSM2644586
40	GSM2644586.sga	CR3|input|None|rep2	input	GSM2644586
41	GSM2644587.centered.sga	T47Dflp|PGR|Ve|rep1	PGR	GSM2644587
42	GSM2644587.sga	T47Dflp|PGR|Ve|rep1	PGR	GSM2644587
43	GSM2644588.centered.sga	T47Dflp|PGR|Ve|rep2	PGR	GSM2644588
44	GSM2644588.sga	T47Dflp|PGR|Ve|rep2	PGR	GSM2644588
45	GSM2644589.centered.sga	T47Dflp|PGR|P4|rep1	PGR	GSM2644589
46	GSM2644589.sga	T47Dflp|PGR|P4|rep1	PGR	GSM2644589
47	GSM2644590.centered.sga	T47Dflp|PGR|P4|rep2	PGR	GSM2644590
48	GSM2644590.sga	T47Dflp|PGR|P4|rep2	PGR	GSM2644590
49	GSM2644591.centered.sga	CR3flp|PGR|Ve|rep1	PGR	GSM2644591
50	GSM2644591.sga	CR3flp|PGR|Ve|rep1	PGR	GSM2644591
51	GSM2644592.centered.sga	CR3flp|PGR|Ve|rep2	PGR	GSM2644592
52	GSM2644592.sga	CR3flp|PGR|Ve|rep2	PGR	GSM2644592
53	GSM2644593.centered.sga	CR3flp|PGR|P4|rep1	PGR	GSM2644593
54	GSM2644593.sga	CR3flp|PGR|P4|rep1	PGR	GSM2644593
55	GSM2644594.centered.sga	CR3flp|PGR|P4|rep2	PGR	GSM2644594
56	GSM2644594.sga	CR3flp|PGR|P4|rep2	PGR	GSM2644594
57	GSM2644595.centered.sga	T47Dflp|input|Ve|rep1	input	GSM2644595
58	GSM2644595.sga	T47Dflp|input|Ve|rep1	input	GSM2644595
59	GSM2644596.centered.sga	T47Dflp|input|Ve|rep2	input	GSM2644596
60	GSM2644596.sga	T47Dflp|input|Ve|rep2	input	GSM2644596
61	GSM2644597.centered.sga	T47Dflp|input|P4|rep1	input	GSM2644597
62	GSM2644597.sga	T47Dflp|input|P4|rep1	input	GSM2644597
63	GSM2644598.centered.sga	T47Dflp|input|P4|rep2	input	GSM2644598
64	GSM2644598.sga	T47Dflp|input|P4|rep2	input	GSM2644598
65	GSM2644599.centered.sga	CR3flp|input|Ve|rep1	input	GSM2644599
66	GSM2644599.sga	CR3flp|input|Ve|rep1	input	GSM2644599
67	GSM2644600.centered.sga	CR3flp|input|Ve|rep2	input	GSM2644600
68	GSM2644600.sga	CR3flp|input|Ve|rep2	input	GSM2644600
69	GSM2644601.centered.sga	CR3flp|input|P4|rep1	input	GSM2644601
70	GSM2644601.sga	CR3flp|input|P4|rep1	input	GSM2644601
71	GSM2644602.centered.sga	CR3flp|input|P4|rep2	input	GSM2644602
72	GSM2644602.sga	CR3flp|input|P4|rep2	input	GSM2644602
73	GSM2644603.centered.sga	ExoR330fs|Ty1|None|rep1	Ty1	GSM2644603
74	GSM2644603.sga	ExoR330fs|Ty1|None|rep1	Ty1	GSM2644603
75	GSM2644604.centered.sga	ExoR330fs|Ty1|None|rep2	Ty1	GSM2644604
76	GSM2644604.sga	ExoR330fs|Ty1|None|rep2	Ty1	GSM2644604
77	GSM2644605.centered.sga	ExoR330fs|input|None|rep2	input	GSM2644605
78	GSM2644605.sga	ExoR330fs|input|None|rep2	input	GSM2644605
79	GSM2644606.centered.sga	ExoR330fs|input|None|rep1	input	GSM2644606
80	GSM2644606.sga	ExoR330fs|input|None|rep1	input	GSM2644606
81	GSM2644607.centered.sga	T47Dflp|PolII|Ve|rep1	PolII	GSM2644607
82	GSM2644607.sga	T47Dflp|PolII|Ve|rep1	PolII	GSM2644607
83	GSM2644608.centered.sga	T47Dflp|PolII|Ve|rep2	PolII	GSM2644608
84	GSM2644608.sga	T47Dflp|PolII|Ve|rep2	PolII	GSM2644608
85	GSM2644609.centered.sga	T47Dflp|PolII|P4|rep1	PolII	GSM2644609
86	GSM2644609.sga	T47Dflp|PolII|P4|rep1	PolII	GSM2644609
87	GSM2644610.centered.sga	T47Dflp|PolII|P4|rep2	PolII	GSM2644610
88	GSM2644610.sga	T47Dflp|PolII|P4|rep2	PolII	GSM2644610
89	GSM2644611.centered.sga	CR3flp|PolII|Ve|rep1	PolII	GSM2644611
90	GSM2644611.sga	CR3flp|PolII|Ve|rep1	PolII	GSM2644611
91	GSM2644612.centered.sga	CR3flp|PolII|Ve|rep2	PolII	GSM2644612
92	GSM2644612.sga	CR3flp|PolII|Ve|rep2	PolII	GSM2644612
93	GSM2644613.centered.sga	CR3flp|PolII|P4|rep1	PolII	GSM2644613
94	GSM2644613.sga	CR3flp|PolII|P4|rep1	PolII	GSM2644613
95	GSM2644614.centered.sga	CR3flp|PolII|P4|rep2	PolII	GSM2644614
96	GSM2644614.sga	CR3flp|PolII|P4|rep2	PolII	GSM2644614

Notes on samples nomenclature:

You should describe here what the sample description field in the table means. Delete this part if not needed

Merged samples:

ATACseq data have been split into two types of reads (samples named 'short' and 'long'):

Short: contain only fragments shorter than 100bp

Ling: contain only fragment between 140 and 260bp (mononucleosomes)

Short reads are oriented whereas long reads have been centered.

• Strand correlation plots: takaku18_strand_cor.pdf
• ESR1 ChIP-seq tag enrichment around bound ESR1 motifs: takaku18_ESR1_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).

• Takaku M, Grimm SA, Roberts JD, Chrysovergis K, Bennett BD, Myers P, Perera L, Tucker CJ, Perou CM, Wade PA
  GATA3 zinc finger 2 mutations reprogram the breast cancer transcriptional network. Nat Commun. 2018 Mar 13;9(1):1059. doi: 10.1038/s41467-018-03478-4. 29535312
• GEO series GSE99479: A class of GATA3 mutation reprograms the breast cancer transcriptional network through gain and loss of function