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| Status |
Public on Oct 20, 2023 |
| Title |
Wild-type_heart_CaptureHiC_rep2 |
| Sample type |
SRA |
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| Source name |
heart
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| Organism |
Mus musculus |
| Characteristics |
tissue: heart
genotype: Wild-type
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
We used the Arima HiC kit to process mouse testis and heart tissues. Briefly, frozen tissue was lysed and conditioned before chromatin digestion. The digested chromatin was then filled in and biotinylated before ligation. Next, chromatin was protein-digested and reverse crosslinking overnight, followed by purification. The purified DNA was then sonicated using the bioruptor pico (Diagenode) and size selected before library preparation using the NEB DNA Ultra II, following Arima’s protocol.
The Hi-C DNA was bound to streptavidin beads before enzymatic end prep, adaptor ligation, DNA release by heat incubation, and lastly, PCR to barcode and amplify the libraries. Capture Hi-C libraries were generated by using the Agilent SureSelect Target Enrichment Kit.
capture Hi-C
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw capture HiC data was aligned to mm10 genome using HiCUP.
Pairtools was used to further process data and generate interaction matrices across replicates in each genotype.
HiCExplorer python package was used to identify TADs and calculate insulation scores.
Assembly: mm10
Supplementary files format and content: bedgraph files contain insulation scores, which are the result of calling TADs on the replicate-merged, normalized, HiC data using the program hicFindTADs, from the HiCExplorer python package.
Supplementary files format and content: (.cool) Cooler files represent replicate-merged HiC matrices at 10kb resolution with Knight-Ruiz Iterative Correction (IC) normalization.
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| Submission date |
Jun 29, 2023 |
| 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 |
GPL24247 |
| Series (1) |
| GSE197926 |
TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function |
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| Relations |
| BioSample |
SAMN36084151 |
| SRA |
SRX20832374 |
| 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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