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| Status |
Public on Aug 14, 2024 |
| Title |
breast cancer single cell A013 |
| Sample type |
SRA |
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| Source name |
MCF7
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: immortalized breast epithelial cell line
treatment: untreated
analysis: single-cell Hi-C
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| Treatment protocol |
Untreated
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| Growth protocol |
Routine cell media for all cell lines, respectively.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of cell nucleus and DNA were performed as described (Flyamer et al. 2017, doi:10.1038/nature21711).
single-cell Hi-C was performed as described (Flyamer et al. 2017, doi:10.1038/nature21711).
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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 |
The raw reads of scHi-C were first aligned to human HG19 genome, then filtered by HiC-Pro to get the valid pairs.
Genome_build: HG19
Supplementary_files_format_and_content: the column headers of *allValidPairs are:
read_name, chromosome of first locus, read position of first locus (currently middle of the reads), strand of first locus, chromosome of second locus, read position of second locus, strand of second locus, DNA fragment length, name of first restriction fragment, name of second restiction fragment, mapping quality of first read, mapping quality of second read, allele-specific analysis
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| Submission date |
Jan 25, 2022 |
| Last update date |
Aug 14, 2024 |
| Contact name |
Yufan Zhou |
| Organization name |
UT health Science Center at San Antonio
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| Street address |
7703 Floyd Curl Dr
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| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (2) |
| GSE194308 |
3D chromatin architecture of drug-tolerant cancer cells at single-cell resolution [scHi-C] |
| GSE195611 |
3D chromatin architecture of drug-tolerant cancer cells at single-cell resolution |
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| Relations |
| BioSample |
SAMN25241856 |
| SRA |
SRX13896436 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5832931_A013.allValidPairs.txt.gz |
35.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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