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| Status |
Public on May 10, 2023 |
| Title |
MCF10DCIS,P6,cHiC |
| Sample type |
SRA |
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| Source name |
MCF10DCIS
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10DCIS
replicate: rep2
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| Treatment protocol |
The media was changed on all cells 24 hours prior to harvesting and grown to ~90% confluence.
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| Growth protocol |
MCF10DCIS were grown in DMEM/F12 (Corning 10-090-CV) supplemented with 5% horse serum (Gibco 16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882) + 20ng/ml hEGF (PeprotechAF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888), Pen/Strep, and L-Glutamine. MCF10CA1a were grown in DMEM/F12 (Corning 10-090-CV) supplemented with 5% horse serum (Gibco 16050 lot #1075876), Pen/Strep, and L-Glutamine. These cells were all grown in a humidified atmosphere with 5% CO2 at 37oC.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C was performed as previously described (Belton et al., 2012) and capture probes were designed in collaboration with Agilent. The capture procedure was performed as per the manufacturer's instructions.
Cells were fixed with 1% methanol free formaldehyde for 10′ at room temperature, treated with glycine on ice for 15 minutes, PBS rinsed, and snap frozen in liquid nitrogen. HINDIII restriction digested products were blunt ligated after incorporation of biotinylated dCTP. The DNA was sonicated and crosslinks were reversed. Beads were used to pull down biotinylated di-tags. Sheered ends were repaired, A-tailed, and barcoded adapters were ligated. High ligation efficiency was determined by nhel restriction digestion (blunt end formation creates a nheI site). The Belton et al., 2012 protocol was modified to increase the ligation step to 10 hours with a second spike-in of t4 ligase at hour 4. We found a dramatic increase in ligation efficiency using these conditions.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
capture HiC
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| Data processing |
HiC-Pro (v 2.8.1_devel PMID: 26619908) was used to process and align reads (bowtie2 v 2.1.0 PMID: 22388286) to canonical chromosomes in hg38.
For visualization, .hic files were generated from allValidPairs files using the hicpro2juicebox.sh utility script included with HiC-pro to match resolutions in the hTERT-RPE1 and U2OS cells.
Supplementary files format and content: Supplementary file contains capture regions and compatible .hic files derived from HiC data in GSE98552 (ENCFF876OWE for hTERT-RPE1 and GSE141139 for USOS .hic files were also used but otherwise available).
Supplementary files format and content: .hic files were generated using HiC-Pro's hicpro2juicebox.sh script. They can be extracted using straw utility from JuiceBox software or strawr R package.
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| Submission date |
Apr 10, 2023 |
| Last update date |
May 10, 2023 |
| Contact name |
Joseph R Boyd |
| Organization name |
University of Vermont
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| Department |
Biomedical and Health Sciences
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| Lab |
Frietze
|
| Street address |
University of Vermont
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| City |
Burlington |
| State/province |
Vermont |
| ZIP/Postal code |
05405 |
| Country |
USA |
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| Platform ID |
GPL18460 |
| Series (2) |
| GSE229296 |
Long-range genomic contacts and spatiotemporal chromatin landscape of human histone gene clusters at Histone Locus Bodies during the cell cycle in breast cancer [cHiC] |
| GSE229297 |
Long-range genomic contacts and spatiotemporal chromatin landscape of human histone gene clusters at Histone Locus Bodies during the cell cycle in breast cancer |
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| Relations |
| SRA |
SRX19917956 |
| BioSample |
SAMN34129854 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7158146_MCF10DCIS_P6_allValidPairs.hic |
496.3 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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