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| Status |
Public on Dec 01, 2020 |
| Title |
HiC_T47DTamR+sapitinib_rep2 |
| Sample type |
SRA |
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| Source name |
HiC_T47DTamR+sapitinib
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| Organism |
Homo sapiens |
| Characteristics |
cell line background: T47D
cell type: breast cancer cell line
phenotype: tamoxifen resistant
restriction enzyme: HindIII
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| Treatment protocol |
MCF7TR or T47DTR cells were cultured in phenol red free RPMI-1640 containing 10% charcoal-stripped FBS, 1% pen/strep and 100nM Tamoxifen (Sigma-Aldrich). Tamoxifen was replaced every 48 hours. All the cells were kept at cell culture incubator with 37 °C and 5% CO2 until they reach 90% confluence. The cells were treated with Sapitinib (AZD8931) at the concentrations at 0uM to 30uM, the gradient concentration is 5uM. Cells absorbance was recorded at day 1 and day 7.
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| Growth protocol |
Human breast carcinoma cell lines MCF7 and T47D and their tamoxifen resistant (TR) cell lines were originated from Osborne et al (Osborne et al. 1994). MCF7 or T47D was cultured in RPMI-1640 supplemented with 10 % fetal bovine serum, 1% penicillin and streptomycin (pen/strep) until 90% confluent.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
In situ Hi-C experiments were performed as described previously (Rao et al, 2015; Zhou et al, 2020). The breast cancer cells were crosslinked with 1% formaldehyde and lysed with ice cold lysis buffer (10mM Tris-Hcl pH 8.0, 10mM NaCl, 0.2 % NP-40, 1mM DTT) to collect nuclei. The pelleted nuclei were digested with 200 units of HINDIII (NEB, R3104L) at 37°C overnight. The restriction fragment overhangs were filled with biotin-labelled dATP (Life Technologies,19524-016) in a Klenow end-filling reaction. Four hundred units of T4 DNA Ligase (NEB, M0202) was added for ligation and samples were incubated for 4 h at room temperature with slow rotation.
The ligation products were purified, and the chromatin was sheared to a size of 300-500bp using Covaris sonicator (Covaris Woburn, MA). Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65601) were used to pull down the Biotin-labelled DNA. The end repair, dA tailing was performed and ligated with Illumina TruSeq adapters to form the final Hi-C ligation products. Each Hi-C library was amplified with 12 cycles of PCR using Illumina primers. The Hi-C library was purified and then sequenced with Illumina HiSeq3000.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
All raw reads were mapped to HG19 reference genome by using HiCUP.
HOMER (Heinz et al. 2010) was used to obtain HI-C interaction matrices with default parameters and 40Kb tiling window size.
The significant interactions (SIFs) were further mapped to promoter and distal regionsbased on UCSC RefSeq HG19 where the mapping definition was used in our previous studies (Gerrard et al, 2019; Zhou et al, 2019).
SIFs and P1D1/2 looping genes were compared by using an in-house python code to obtain DLGs
TopDom (Shin et al 2016) was used to identify TAD, boundary, and gap for intra-chromosomal interactions
Genome_build: hg19
Supplementary_files_format_and_content: xlsx;changed TADs files, differential gene loops
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| Submission date |
Jan 28, 2020 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Victor Jin |
| E-mail(s) |
vjin@mcw.edu
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| Phone |
+1 210 562 9209
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| Organization name |
Medical college of Wisconsin
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| Department |
IHE
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| Street address |
8701 Watertown Plank Rd
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| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (2) |
| GSE144377 |
The 3D Genomic Landscape of Differential Response to EGFR/HER2 Inhibition in Endocrine-Resistant Breast Cancer [HiC] |
| GSE144380 |
The 3D Genomic Landscape of Differential Response to EGFR/HER2 Inhibition in Endocrine-Resistant Breast Cancer |
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| Relations |
| BioSample |
SAMN13936274 |
| SRA |
SRX7642872 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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