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).



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.

    Quality Control and Analysis

    Technical Notes

    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).


    Last update: 17 Jul 2019