Evidence map›Paper›PMID 39930187›Full record

ReviewAdvances in experimental medicine and biology2025

Progress in Assessing Retinal Microglia Using Single-Cell RNA Sequencing.

Sarah J Karlen, Kaitryn E Ronning, Marie E Burns

Abstract readReview
PubMed Publisher
In one paragraph

Review in Advances in experimental medicine and biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Sarah J KarlenDepartment of Cell Biology and Human Anatomy, University of California Davis, Davis, CA, USA.
Kaitryn E RonningSorbonne Université, CNRS, Inserm, Institut de la Vision, Paris, France.
Marie E BurnsDepartment of Cell Biology and Human Anatomy, University of California Davis, Davis, CA, USA. meburns@ucdavis.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Retinal degeneration is the leading cause of both inherited and age-related vision loss, and often leads to neuroimmune activation and a heterogeneous population of microglia and monocyte-derived macrophages. A common method to study the innate immune response during retinal degeneration is single-cell RNA sequencing, but the best way to obtain and analyze these cells over the course of degeneration remains debated. Here, we compare two common methods of retinal cell preparation (collagenase digestion with immune cell enrichment by FACS; Col/FACS vs papain digestion of the whole retina without enrichment; Pap/Whole) and three different algorithms for database integration (CCA, RPCA, and Harmony) to examine microglia in healthy retinas. We find that the Pap/Whole dissociation produced a smaller fraction of activated microglial cells and that the Harmony integration of microglia isolated by these two methods resulted in the highest Silhouette score, indicating the greatest separation of microglia subclusters from these data sets.

Indexed as

MicrogliaRetinaRetinal DegenerationSequence Analysis, RNASingle-Cell AnalysisAnimalsHumansRNA-SeqDataset integrationMicrogliaNeuroinflammationRetinal dissociationscRNAseqTranscriptome

Identifiers

PMID39930187

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.