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Status |
Public on May 22, 2024 |
Title |
Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +24h @RT |
Sample type |
SRA |
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Source name |
muscle
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Organism |
Bos taurus |
Characteristics |
tissue: muscle treatment: Beef cheek, +24h @RT
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Extracted molecule |
genomic DNA |
Extraction protocol |
The protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024. Briefly, PaleoHi-C is a a modified in situ Hi-C protocol, tailored towards working with highly degraded samples. The principal modifications were: (i) immediate preservation in the field using ethanol to reduce microbial activity; and (ii) sequestration of chromatin bodies on beads; (iii) removal of shearing and size selection given the lack of high molecular weight DNA; and (iv) library amplification using a paleo-compatible workflow Library contruction protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024. Modified Hi-C.
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Library strategy |
Hi-C |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 550 |
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Description |
HIC17032.hic HIC17032_30.hic
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Data processing |
Hi-C-guided genome assembly (3D-DNA, JBAT) Reference-guided 3D genome assembly (Anonamos, 3D-DNA, JBAT) Construction of the chromosome-length Hi-C contact map (BWA, Juicer, 3D-DNA) liftover (KentUtils, 3D-DNA) Gene annotation (TOGA) Compartment annotation (CRUSH) Loop calling and aggregate analysis (HiCCUPS, Juicer Tools, SIP, SIP META) Aggregate chromosome analysis (3D-DNA) Modeling of 3D structures of woolly mammoth chromosomes (OpenMiChroM) DNA degradation simulations (NuChroM, custom script) Assembly: The following existing genome builds were used in parts of the study: Loxafr3.0 (GCA_000001905.1), ASM1433276v1 (GCA_014332765.1), EquCab2.0 (GCF_000002305.2), ASM303372v1 (GCA_003033725.1), bosTau9 (GCF_002263795.3), ASM651725v1 (GCF_006517255.1), ASM3043605v1 (GCF_030436055.1), ASM331443v2 (GCF_003314435.2), hg38, hg19. Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly Supplementary files format and content: hic: contact maps generated by aligning Hi-C data to reference sequences. In addition to "standard" hic maps build against chromosome-length references included are "assembly" maps generated by 3D-DNA for before and after genome assembly and an aggregate chromosome analysis (ACA) map. Supplementary files format and content: bedpe: chromatin loops Supplementary files format and content: bedgraph: A/B compartment annotations Supplementary files format and content: sw: HDF5-based file for storing 3D structure ensembles Supplementary files format and content: assembly: text file describing the relationship between the draft assembly and the chromosome-length upgrade Supplementary files format and content: bed: gene annotations
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Submission date |
May 21, 2024 |
Last update date |
May 22, 2024 |
Contact name |
Olga Dudchenko |
E-mail(s) |
Olga.Dudchenko@bcm.edu
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Organization name |
Baylor College of Medicine
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Street address |
1 Baylor Plaza
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City |
Houston |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
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Platform ID |
GPL27907 |
Series (1) |
GSE268050 |
Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample |
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Relations |
BioSample |
SAMN41403633 |
SRA |
SRX24562034 |
Supplementary data files not provided |
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Raw data are available in SRA |
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