NTR: SPRITE assay

[bonitalam]

Hello, the ENCODE project has another NTR request for an assay that we will need to annotate a number of experiments.

editor preferred term: Split-pool recognition of interactions by tag extension alternate terms: SPRITE textual definition: SPRITE is an assay that enables genome-wide detection of multiple simultaneously occurring higher-order DNA interactions within the nucleus, providing resolution of interchromosomal spatial arrangement around nuclear bodies. SPRITE requires crosslinking of DNA, RNA, and protein in cells. Chromatin from isolated nuclei is fragmented and interacting molecules of individual complexes are barcoded using a split-pool strategy allowing identification of these interactions by sequencing and matching reads with the same barcode. definition source for the textual definition: https://www.ncbi.nlm.nih.gov/pubmed/29887377 logical definition: chromosome conformation capture assay (OBI:0002439) —> SPRITE

[ddooley]

Will investigate the definition as per source paper.

[ddooley]

Both OBI and EFO have an existing hierarchy that include "chromosome conformation capture assay": EFO:

OBI:

This exposes an OBI class issue, that there are chromosome conformation capture assays that are ligation free. Suggests moving this class up one level in hierarchy.

EFO also has this existing definition for SPRITE, along with two subclasses specialized for DNA and DNA-RNA interaction detection:

SPRITE (split-pool recognition of interactions and tag extension) is an assay designed to detect multi-way interactions between nucleic acids. The procedure involves crosslinking nuclei, and then splitting the lysate among wells in a 96-well or other multi-well plate. A different barcode is ligated to the fragments in each well, and the lysates are pooled together again. This sequence of splitting, tagging, and re-combining is repeated several times so that fragments with the same sequences of barcodes represent fragments that have co-associated throughout the experiment. Finally, a sequencing library is constructed and high-throughput sequencing is performed.