NAISS
SUPR
NAISS Projects
SUPR
Chromatin organisation and public-data copy-number quality control
Dnr:

NAISS 2026/4-1699

Type:

NAISS Small

Principal Investigator:

Wenjing Kang

Affiliation:

Karolinska Institutet

Start Date:

2026-09-25

End Date:

2027-10-01

Primary Classification:

10610: Bioinformatics and Computational Biology (Methods development to be 10203)

Webpage:

Allocation

Abstract

Genomic loci positioning by sequencing (GPSeq) profiles the radial organisation of chromatin by inferring the distance from genomic loci to the nuclear lamina. GPSeq relies on gradual restriction digestion of chromatin from the nuclear lamina toward the nucleus centre, followed by sequencing of the generated cut sites. Using this technology we study how chromatin is organised inside the nucleus, how that organisation differs between cell types, and how chromatin remodelling affects gene expression. The project integrates GPSeq with complementary assays (RADICL-seq, Hi-C, RNA-seq, CAGE, ChIP-seq, ATAC-seq) across iPSC differentiation into neural stem cells and cortical neurons. The immediate driver of this request is a second, time-limited line of work: a public resource for cell-line karyotype quality control. Copy-number aberrations are stable, cell-line-specific fingerprints, and we have shown they are recoverable from ordinary ChIP-seq input/control samples without any dedicated assay. This makes it possible to ask, for every widely used human cell line, whether independent laboratories have deposited samples carrying different copy-number profiles — the "same name, different genome" problem that silently undermines reproducibility. The resource will let a researcher look up a cell line, see where genomes differ between laboratories, and follow links back to the original accessions. It reuses existing public data and generates none. Preprocessing the corpus is a bounded, three-month computational task; the request is sized to complete it.