Real microscopy · genome-wide RNAi screen
Which genes change DNA-damage foci in human cells?
An explorer for a published screen that silenced 17,536 human genes one at a time and counted 53BP1 foci, the bright spots that mark DNA double-strand breaks. All numbers are the authors' own measurements; the images are the original microscopy.
53BP1 foci mark DNA breaks anywhere in the genome, not telomeres specifically. This site is a companion to Telomere Evolution Lab; the link between the two is qualitative (see below). Have your own microscopy image? Try our simple, unvalidated counter on the Analyze your image page.
What the screen found
Each gene's median score z: how many control-spreads its wells sit from the negative controls (negative = fewer 53BP1 foci). Only genes with at least two wells can be ranked.
How to read these numbers
Gene explorer
Search any of the screened genes by symbol or Ensembl ID (aliases and previous names too, when the HGNC table is available). Values come from the gene's quality-controlled wells; a gene needs two wells and two siRNAs before it can be called a hit.
Test your gene list
Paste a list of genes and see where they sit in this screen: a table, a volcano plot, a rank plot and two simple enrichment tests. Exploratory only (see the caveats below the results).
Telomere and shelterin genes
The screen also silenced telomerase and shelterin genes. None of the rankable ones is a supported hit in this short-term screen.
An honest null: the screen measured foci shortly after siRNA transfection, before telomere erosion could build up. Telomere dysfunction foci typically need longer or targeted assays (for example TRF2 dominant-negative), so a flat result here is expected rather than evidence that these genes do not matter.
Original images
One microscope field per well. Blue: DNA (Hoechst). Green: 53BP1. Toggle our automatic outline to see which nuclei and spots our classical counter picked up.
Caution on pairing: each image is shown for the IDR well that carries that gene's annotation. Our follow-up analysis (Experiment L2 below) suggests that link may be off for some wells, so the image next to a well's numbers is an illustration of the screen, not evidence for that gene's value. The numbers are the authors' table.
Experiment L: can a simple counter reproduce the authors' numbers?
Our classical pipeline (background-corrected Otsu nuclei, top-hat local maxima for foci) on the single IDR image of each well, against the authors' published per-well foci per cell. Negative result, kept on purpose.
Data, export and citation
Everything on this site is computed from open data. Download the processed tables, or copy a citation for exactly what you are looking at.
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Cite this view
BibTeX for the paper
How this connects to Telomere Evolution Lab
In the model
Telomere Lab's genome-stability layer gives every cell a mutation_burden and an apoptosis checkpoint. Its Experiment K shows that a clone which loses the checkpoint takes over a culture, because nothing culls its damaged cells.
In this screen
53BP1 foci are a real, per-cell readout of unrepaired breaks. The screen shows which genes raise that burden (proteasome) and which remove the cell's ability to mark it (RNF8, RNF168, MDC1), which is the recruitment step a damage checkpoint relies on.
This is a qualitative bridge. The screen does not calibrate any model parameter, and the model does not predict these measurements.