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| Status |
Public on Dec 11, 2019 |
| Title |
Hi-C MCF7 Replicate 2 |
| Sample type |
SRA |
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| Source name |
MCF7
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: breast cancer cells
resistant phenotype: responsive
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| Growth protocol |
MCF7 breast cancer cells, and the corresponding endocrine resistant sub cell lines were kindly given to our laboratory by Dr Julia Gee (Cardiff University, UK). MCF7 cells were maintained in RPMI-1640 based medium containing 5% (v/v) fetal calf serum (FCS). Tamoxifen-resistant MCF7 (TAMR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and 4-OH-tamoxifen (1×10－7 M) (TAM). Fulvestrant-resistant MCF7 (FASR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and fulvestrant (1×10－7 M) (FAS). Endocrine resistant sub lines were established and characterised following 6 months endocrine challenge. All cell lines were authenticated by short-tandem repeat (STR) profiling (Cell Bank, Australia) and cultured for less than 6 months after authentication.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with formaldehyde, lysed and the intact nuclei was permeabilized. DNA was then cut with NcolI restriction enzyme, the overhangs filled in incorporating a biotinylated base and the free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and the biotinylated ligation junctions were pulled down with streptavidin beads.
Custom library construction protocol was followed. Briefly, DNA was end-repaired and dA-tailing using the NEBNext DNA Master Mixes kit and the ligation of universal adapter was performed on Streptavidin-bound DNA using the NEBNext Ultra DNA Library Prep kit. After adapter ligation DNA was PCR amplified with indexed Illumina primers for 8-12 cycles and library fragments of at least 200bp were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
TKCC_MCF7_NcolII_2
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| Data processing |
Raw sequence data was mapped and processed using HiC-Pro v2.7.7 (Servant et al., 2015). The paired end reads were aligned separately using bowtie2 against the hg38 human build. Contact matrices were constructed at multiple resolutions and normalized suing ICE normalization algorithm (Imakaev et al. 2012).
Juicebox hic files were prepared using hicpro2juicebox script (Servant et al., 2015). Topologically Associating Domains were annotated using domain-caller (Dixon et al., 2012). Sub-compartments A and B were annotated using Homer Sub-nuclear Compartment Analysis (Heinz et al., 2010). Differential interactions were identified using diffHiC v1.8.1 (Lun et al., 2015) at 20kb resolution.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: allValidPairs files contain all valid interactions identified at multiple resolutions (10kb, 20kb, 40kb, 150kb, 500kb and 1Mb) using HiC-Pro pipeline. The validPairs are stored using a tab-delimited text format as described in (Servant et al., 2015). hic files contain compressed contact matrices at all resolutions. hic format can also be used to visualise Hi-C data in Juicebox (Durand et al., 2016; Robinson et al., 2018) or WashU Epigenome Browser (Zhou et al., 2013). TADs.txt files contain domain calls generated via domain-caller in a bed format. pcaOut files contain sub-nuclear compartment calls created by Homer software. DIs.tsv files contain all differential interactions identified by diffHic (Lun et al., 2015) at 20kb resolution.
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| Submission date |
Aug 17, 2018 |
| Last update date |
Dec 13, 2019 |
| Contact name |
Joanna Achinger-Kawecka |
| E-mail(s) |
j.achinger@garvan.org.au
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| Organization name |
Garvan Institute of Medical Research
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| Lab |
Epigenetics Research Laboratory
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| Street address |
384 Victoria Street
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| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE118712 |
Epigenetic reprogramming at estrogen-receptor binding sites alters the 3D chromatin landscape in endocrine resistant breast cancer [Hi-C] |
| GSE118716 |
Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine resistant breast cancer |
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| Relations |
| BioSample |
SAMN09848872 |
| SRA |
SRX4564981 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3336891_MCF7_2_allValidPairs.hic |
1.3 Gb |
(ftp)(http) |
HIC |
| GSM3336891_MCF7_2_allValidPairs.txt.gz |
2.7 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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