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Data of: Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts

Citation

Hirata, Yoshito et al. (2022), Data of: Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts, Dryad, Dataset, https://doi.org/10.5061/dryad.3j9kd51hv

Abstract

These files are results obtained in
Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts
by Yoshito Hirata, Arisa H. Oda, Chie Motono, Masanori Shiro & Kunihiro Ohta.

There are 33 files for the corresponding each reconstruction of three-dimensional chromosomone structures
for each cell.
There are 3D structures for 15 GM cells and 18 PBMC cells, which are obtained from the single cell Hi-C data of Tan et al. Science (2018).

For each file, there are 6 columns:
The first column corresponds to the allele (0: maternal, 1: paternal)
The second column corresponds to the chromosome (1-22: chromosome's number, 23: X, 24: Y)
The third column corrsponds to the base point.
The fourth column, the fifth column and the sixth column correspond to x-, y-, and z-axes of our reconstruction.

Methods

First, the single cell Hi-C data of Tan et al. (2018) have been downloaded from

through GEO Series accession number GSE117876 at www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117876

Then, we applied the proposed recurrence plot-based method here to

reconstruct 3D chromosome structures of 33 cells (15 GM cells and 18 PBMC cells).

The resulting 3D chromosome structures are deposited here.

Usage Notes

Each file represents the 3D chromosome structure for each cell.

For each file, there are 6 columns to represent 3D structure:
The first column corresponds to the allele (0: maternal, 1: paternal)
The second column corresponds to the chromosome (1-22: chromosome's number, 23: X, 24: Y)
The third column corrsponds to the base point.
The fourth column, the fifth column and the sixth column correspond to x-, y-, and z-axes of our reconstruction.

Funding

AMED, Award: JP22gm1310004

Japan Science and Technology Agency, Award: JPMJCR18S3