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

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.

• Raw data was downloaded from: GSE112852
• Input file format: SRA
• Download date: 26-1-2021

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.

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).

• Klotz R, Thomas A, Teng T, Han SM, Iriondo O, Li L, Restrepo-Vassalli S, Wang A, Izadian N, MacKay M, Moon BS, Liu KJ, Ganesan SK, Lee G, Kang DS, Walmsley CS, Pinto C, Press MF, Lu W, Lu J, Juric D, Bardia A, Hicks J, Salhia B, Attenello F, Smith AD, Yu M.
  Circulating Tumor Cells Exhibit Metastatic Tropism and Reveal Brain Metastasis Drivers. Cancer Discov. 2020 Jan;10(1):86-103. doi: 10.1158/2159-8290.CD-19-0384. Epub 2019 Oct 10. 31601552
• GEO series GSE112852: Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [ATAC-seq]