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| Status |
Public on Apr 01, 2024 |
| Title |
MCF7_H3K27ac_HiChIP_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 carcinoma cell line
hichip antibody: H3K27ac (Abcam ab4729)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
HiChIP protocol (Mumbach et al., 2016, Nature Methods) to enrich DNA fragments that are in proximity with each other
Illumina Tagment DNA Enzyme and Buffer Kit (Illumina 20034197)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
HiC-Pro to align sequencing reads
hichipper to identify chromatin loops connecting H3K27ac anchors
Assembly: hg19
Supplementary files format and content: intra-chromosomal interaction counts text file in bedpe format. Rows are interactions (loops). Columns are chromosome1, start1, end1, chromosome2, start2, end2, FDR (blank), PETs
Supplementary files format and content: inter-chromosomal interaction counts text file in bedpe format. Rows are interactions (loops). Columns are chromosome1, start1, end1, chromosome2, start2, end2, FDR (blank), PETs
Library strategy: HiChIP
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| Submission date |
Mar 27, 2023 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Xiaoyang Zhang |
| E-mail(s) |
xiaoyang.zhang@hci.utah.edu
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| Organization name |
University of Utah
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| Department |
Oncological Sciences
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| Lab |
Zhang
|
| Street address |
1950 Circle of Hope Drive
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| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE228246 |
3D genomics analysis identifies enhancer hijacking caused by structural alterations and extrachromosomal circular DNA formation [HiChIP] |
| GSE228247 |
3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression |
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| Relations |
| BioSample |
SAMN33926736 |
| SRA |
SRX19782090 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7117678_MCF7_H3K27ac_HiChIP_rep1.inter.loop_counts.bedpe.gz |
3.2 Mb |
(ftp)(http) |
BEDPE |
| GSM7117678_MCF7_H3K27ac_HiChIP_rep1.intra.loop_counts.bedpe.gz |
1.9 Mb |
(ftp)(http) |
BEDPE |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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