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| Status |
Public on Oct 20, 2023 |
| Title |
pahari_mouse_F_HiC |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus pahari |
| Characteristics |
tissue: Liver
common_name: Shrewlike Mouse
protocol: Arima
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Arima HiC
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
HiC data were subject to quality control and alignment with bowtie2 using the HiCUP pipeline.
Bam files were paired and converted to .cool format using cooltools.
TADs were called using HicExplorer, HicFindTADs with parameters --minDepth 100000, --maxDepth 600000, --delta 0.01, --correctForMultipleTesting fdr
Supplementary_files_format_and_content: BED files with TAD boundary regions
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| Submission date |
Mar 04, 2022 |
| Last update date |
Oct 20, 2023 |
| Contact name |
Mariam Okhovat |
| Organization name |
Oregon Health and Science University
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| Department |
Medicine
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| Street address |
3030 S Moody Ave.
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| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| Platform ID |
GPL32023 |
| Series (1) |
| GSE197926 |
TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function |
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| Relations |
| BioSample |
SAMN26437306 |
| SRA |
SRX14371668 |
| 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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