Protocol for immunofluorescence detection and quantitative analysis of pH-dependent transcriptional condensates.

Zhongyang Wu, Krishnan Raghunathan, Zhe Zhong, Jay Thiagarajah, Xu Zhou

Abstract read

In one paragraph

Article in STAR protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

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0citing papers in PubMed

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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

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3 · Its place in the literature

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0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

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5 · Who and what money

Authors and funding

5 authors.

Zhongyang WuDivision of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.

Krishnan RaghunathanDivision of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.

Zhe ZhongDivision of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.

Jay ThiagarajahDivision of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.

Xu ZhouDivision of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA. Electronic address: xu.zhou@childrens.harvard.edu.

Funding

Understanding Immune-Stromal Interactions in Tissue Homeostasis and InflammationR35GM151000 · NIGMS · BOSTON CHILDREN'S HOSPITAL · PI XU ZHOU · 2023 to 2026

$1.8M

NIGMS NIH HHS R35 GM151000

6 · The paper itself

Abstract

Acidic pH regulates the assembly of transcriptional condensates containing BRD4 and MED1 in a variety of mouse and human cells. Here, we present a protocol to image and quantify BRD4 condensates in bone marrow-derived macrophages. We describe steps for preparing macrophage growth medium at controlled pH levels, performing immunofluorescence experiments, and acquiring images with Airyscan confocal and STED super-resolution microscopy. We detail image processing pipelines to analyze condensate properties using FIJI, CellProfiler, and a custom MATLAB program. For complete details on the use and execution of this protocol, please refer to Wu et al.

Indexed as

Biomolecular CondensatesFluorescent Antibody TechniqueTranscription, GeneticAnimalsHumansHydrogen-Ion ConcentrationImage Processing, Computer-AssistedMacrophagesMiceNuclear ProteinsTranscription FactorsNuclear ProteinsTranscription FactorsCell cultureImmunologyMicroscopy

Identifiers

PMID41818234

DOI10.1016/j.xpro.2026.104425

PMCPMC12994006

What OpenQuestion holds

Textmetadata

LicenceCC BY

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Registered trials

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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.