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.