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| Status |
Public on Mar 27, 2024 |
| Title |
MCF7_rep1 |
| 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
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| Treatment protocol |
None
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| Growth protocol |
MCF7 human breast cancer cell lines have been cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% Fetal Bovine Serum (FBS-12A, Capricorn Scientific) and penicillin/streptomycin (100μg/mL, Gibco). Cell lines were subjected to regular Mycoplasma testing, and underwent authentication by short tandem repeat profiling (Eurofins Genomics).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C single-index library preparation of MCF7 cells was performed as previously described [Donaldson-Collier, M.C., et al., EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains. Nature Genetics, 2019. 51(3): p. 517-528.] using MboI (New England Biolabs) restriction enzyme.
Single-indexing 75bp Paired-end
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Data processing |
Raw fastq data were analyzed at 10kb resolution using the snHiC pipeline (v0.2.0) [Gregoricchio, S. and W. Zwart, snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis. Bioinformatics Advances, 2023. 3(1)] applying default parameters.
Assembly: Hg19/GRCh37
Supplementary files format and content: .cool, Hi-C contact matrices
Supplementary files format and content: .h5, Hi-C contact matrices
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| Submission date |
Oct 06, 2023 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Wilbert Zwart |
| E-mail(s) |
w.zwart@nki.nl
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| Organization name |
Netherlands Cancer Institute
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| Department |
Oncogenomics
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| Lab |
Hormone-dependent cancers
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| Street address |
Plesmanlaan 121
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| City |
Amsterdam |
| State/province |
Noord-Holland |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
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| Platform ID |
GPL21697 |
| Series (2) |
| GSE244844 |
Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions [Hi-C] |
| GSE244845 |
Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions |
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| Relations |
| BioSample |
SAMN37711686 |
| SRA |
SRX22022160 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7830694_MCF7_rep1_mapQ15_10kb.cool.gz |
69.3 Mb |
(ftp)(http) |
COOL |
| GSM7830694_MCF7_rep1_mapQ15_10kb_normalized_corrected.cool.gz |
117.9 Mb |
(ftp)(http) |
COOL |
SRA Run Selector |
| Raw data are available in SRA |
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