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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 28, 2024 |
| Title |
Hi-C of Bos taurus DNA Zoo Sample6834, DIY sirloin jerky in a food dehydrator, 2.5h, rep2 |
| Sample type |
SRA |
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| Source name |
sirloin
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| Organism |
Bos taurus |
| Characteristics |
tissue: sirloin
treatment: DIY sirloin jerky in a food dehydrator, 2.5h
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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.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
HIC17016+HIC17060.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 |
Jun 27, 2024 |
| Last update date |
Jun 28, 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 |
SAMN42012258 |
| SRA |
SRX25027684 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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