Klotz 2020, ATAC-seq in breast cancer CTC lines and CTC-derived metastases from mice.

Description

ATAC-seq was used to generate chromatin accessibility maps of (i) cell cultures derived from circulating tumor cell (CTC) lines and (ii) CTC-induced metastases recovered from different mouse organs. The parental CTC lines were originally established from patients with metastatic luminal breast cancer. Metastatic samples were recovered from mouse brain, lung and bone after intracardiac inoculation. Second and third generation metastatic samples were obtained by multiple rounds of in vivo selection in mice.

Source

Samples

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

DNase FAIRE data:

Filename Description Feature GEO-ID
1 ATAC-seq_Brx07_parental_CTC_Rep1.sga BC-CTC Brx07|ATAC-seq|parental|rep1 ATACseq GSM3089837
2 ATAC-seq_Brx07_parental_CTC_Rep2.sga BC-CTC Brx07|ATAC-seq|parental|rep2 ATACseq GSM3089838
3 ATAC-seq_Brx07_parental_CTC_Rep3.sga BC-CTC Brx07|ATAC-seq|parental|rep3 ATACseq GSM3089839
4 ATAC-seq_Brx07_parental_CTC_Rep4.sga BC-CTC Brx07|ATAC-seq|parental|rep4 ATACseq GSM3089840
5 ATAC-seq_Brx07_parental_CTC_Rep5.sga BC-CTC Brx07|ATAC-seq|parental|rep5 ATACseq GSM3089841
6 ATAC-seq_Brx07_parental_CTC_disso_Rep7.sga BC-CTC Brx07|ATAC-seq|parental disso|rep7 ATACseq GSM3089842
7 ATAC-seq_Brx07_parental_CTC_disso_Rep8.sga BC-CTC Brx07|ATAC-seq|parental disso|rep8 ATACseq GSM3089843
8 ATAC-seq_Brx07_parental_CTC_Rep6.sga BC-CTC Brx07|ATAC-seq|parental|rep6 ATACseq GSM3089844
9 ATAC-seq_Brx07_Kidney_mets_80_1.sga BC-CTC Brx07|ATAC-seq|kidney-mets 1|80 ATACseq GSM3089845
10 ATAC-seq_Brx07_lung_mets_28_2.sga BC-CTC Brx07|ATAC-seq|lung-mets 2|28 ATACseq GSM3089846
11 ATAC-seq_Brx07_lung_mets_30_2.sga BC-CTC Brx07|ATAC-seq|lung-mets 2|30 ATACseq GSM3089847
12 ATAC-seq_Brx07_lung_mets_71_1.sga BC-CTC Brx07|ATAC-seq|lung-mets 1|71 ATACseq GSM3089848
13 ATAC-seq_Brx07_lung_mets_77_1.sga BC-CTC Brx07|ATAC-seq|lung-mets 1|77 ATACseq GSM3089849
14 ATAC-seq_Brx07_ovary_mets_12_1.sga BC-CTC Brx07|ATAC-seq|ovary-mets 1|12 ATACseq GSM3089850
15 ATAC-seq_Brx07_ovary_mets_24_2.sga BC-CTC Brx07|ATAC-seq|ovary-mets 2|24 ATACseq GSM3089851
16 ATAC-seq_Brx07_ovary_mets_27_2.sga BC-CTC Brx07|ATAC-seq|ovary-mets 2|27 ATACseq GSM3089852
17 ATAC-seq_Brx07_ovary_mets_28_2.sga BC-CTC Brx07|ATAC-seq|ovary-mets 2|28 ATACseq GSM3089853
18 ATAC-seq_Brx07_ovary_mets_30_2.sga BC-CTC Brx07|ATAC-seq|ovary-mets 2|30 ATACseq GSM3089854
19 ATAC-seq_Brx42_parental_CTC_Rep1.sga BC-CTC Brx42|ATAC-seq|parental|rep1 ATACseq GSM3089855
20 ATAC-seq_Brx42_parental_CTC_disso_Rep3.sga BC-CTC Brx42|ATAC-seq|parental disso|rep3 ATACseq GSM3089856
21 ATAC-seq_Brx42_parental_CTC_disso_Rep4.sga BC-CTC Brx42|ATAC-seq|parental disso|rep4 ATACseq GSM3089857
22 ATAC-seq_Brx42_parental_CTC_Rep2.sga BC-CTC Brx42|ATAC-seq|parental|rep2 ATACseq GSM3089858
23 ATAC-seq_Brx42_brain_mets_66_1.sga BC-CTC Brx42|ATAC-seq|brain-mets 1|66 ATACseq GSM3089859
24 ATAC-seq_Brx42_brain_mets_69_1.sga BC-CTC Brx42|ATAC-seq|brain-mets 1|69 ATACseq GSM3089860
25 ATAC-seq_Brx42_brain_mets_74_1.sga BC-CTC Brx42|ATAC-seq|brain-mets 1|74 ATACseq GSM3089861
26 ATAC-seq_Brx50_parental_CTC_Rep1.sga BC-CTC Brx50|ATAC-seq|parental|rep1 ATACseq GSM3089862
27 ATAC-seq_Brx50_parental_CTC_disso_Rep3.sga BC-CTC Brx50|ATAC-seq|parental disso|rep3 ATACseq GSM3089863
28 ATAC-seq_Brx50_parental_CTC_disso_Rep4.sga BC-CTC Brx50|ATAC-seq|parental disso|rep4 ATACseq GSM3089864
29 ATAC-seq_Brx50_parental_CTC_Rep2.sga BC-CTC Brx50|ATAC-seq|parental rep2 ATACseq GSM3089865
30 ATAC-seq_Brx50_bone_mets_83_2.sga BC-CTC Brx50|ATAC-seq|bone-mets 2|83 ATACseq GSM3089866
31 ATAC-seq_Brx50_brain_mets_56_3.sga BC-CTC Brx50|ATAC-seq|brain-mets 3|56 ATACseq GSM3089867
32 ATAC-seq_Brx50_brain_mets_83_2.sga BC-CTC Brx50|ATAC-seq|brain-mets 2|83 ATACseq GSM3089868
33 ATAC-seq_Brx50_brain_mets_84_2.sga BC-CTC Brx50|ATAC-seq|brain-mets 2|84 ATACseq GSM3089869
34 ATAC-seq_Brx68_parental_CTC_Rep3.sga BC-CTC Brx68|ATAC-seq|parental|rep3 ATACseq GSM3089870
35 ATAC-seq_Brx68_parental_CTC_Rep1.sga BC-CTC Brx68|ATAC-seq|parental|rep1 ATACseq GSM3089871
36 ATAC-seq_Brx68_parental_CTC_disso_Rep4.sga BC-CTC Brx68|ATAC-seq|parental disso|rep4 ATACseq GSM3089872
37 ATAC-seq_Brx68_parental_CTC_disso_Rep5.sga BC-CTC Brx68|ATAC-seq|parental disso|rep5 ATACseq GSM3089873
38 ATAC-seq_Brx68_parental_CTC_Rep2.sga BC-CTC Brx68|ATAC-seq|parental|rep2 ATACseq GSM3089874
39 ATAC-seq_Brx68_bone_mets_21_1.sga BC-CTC Brx68|ATAC-seq|bone-mets 1|21 ATACseq GSM3089875
40 ATAC-seq_Brx68_bone_mets_22_1.sga BC-CTC Brx68|ATAC-seq|bone-mets 1|22 ATACseq GSM3089876
41 ATAC-seq_Brx68_bone_mets_26_1.sga BC-CTC Brx68|ATAC-seq|bone-mets 1|26 ATACseq GSM3089877
42 ATAC-seq_Brx68_bone_mets_84_2.sga BC-CTC Brx68|ATAC-seq|bone-mets 2|84 ATACseq GSM3089878
43 ATAC-seq_Brx68_bone_mets_x1_1.sga BC-CTC Brx68|ATAC-seq|bone-mets 1|x1 ATACseq GSM3089879
44 ATAC-seq_Brx68_bonejaw_mets_2_1.sga BC-CTC Brx68|ATAC-seq|bonejaw-mets 1|2 ATACseq GSM3089880
45 ATAC-seq_Brx68_boneleg_mets_2_1.sga BC-CTC Brx68|ATAC-seq|boneleg-mets 1|2 ATACseq GSM3089881
46 ATAC-seq_Brx68_boneleg_mets_2_2.sga BC-CTC Brx68|ATAC-seq|boneleg-mets 2|2 ATACseq GSM3089882
47 ATAC-seq_Brx68_lung_mets_x1_1.sga BC-CTC Brx68|ATAC-seq|lung-mets 1|x1 ATACseq GSM3089883

Notes on samples nomenclature:

Field 1 (source):

  • Brx07, Brx42, Brx50, Brx68 identify different CTC donor patients.
  • Field 3 (condition):

  • "parental disso" : Parental CTC libraries were subjected to the same dissociation protocols used for dissociating metastatic tumor.
  • e.g. "brain-mets 3" : The number 3 indicates that this is a 3rd generation metastasis.
  • Field 4 (replicate):

  • e.g."80" : plain numbers distinguish different metastatic samples of the same type.
  • Technical Notes

    SRA toolkit v2.10.8) and mapped to the genome using bowtie v1.2.2 in paired-end mapping mode. 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 v1.5.4 from ChIP-Seq v1.5.5).

    References

    Last update: 30 Jan 2021