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Related Concept Videos

Using an Automated Cell Counter to Simplify Gene Expression Studies: siRNA Knockdown of IL-4 Dependent Gene Expression in Namalwa Cells10:34

Using an Automated Cell Counter to Simplify Gene Expression Studies: siRNA Knockdown of IL-4 Dependent Gene Expression in Namalwa Cells

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This procedure describes a quick and easy workflow to introduce siRNA into difficult to transfect cell lines and follow gene expression by real-time PCR. Use of an automated cell counter, multi-well electroporation plate, and automated electrophoresis station provide quick and reliable results without the need for expensive robotic...
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Here, we describe a protocol for fine-tuning regions of interest (ROIs) for Spatial Omics technologies to better characterize the tumor microenvironment and identify specific cell populations. For proteomics assays, automated customized protocols can guide ROI selection, while transcriptomics assays can be fine-tuned utilizing ROIs as small as 50 µm.
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Related Experiment Video

Updated: Jan 19, 2026

Using an Automated Cell Counter to Simplify Gene Expression Studies: siRNA Knockdown of IL-4 Dependent Gene Expression in Namalwa Cells
10:34

Using an Automated Cell Counter to Simplify Gene Expression Studies: siRNA Knockdown of IL-4 Dependent Gene Expression in Namalwa Cells

Published on: April 14, 2010

16.0K

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene

Chenglong Xia1,2,3, Jean Fan1,2,3, George Emanuel1,2,3

  • 1Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138.

Proceedings of the National Academy of Sciences of the United States of America
|September 11, 2019
PubMed
Summary

Multiplexed error-robust fluorescence in situ hybridization (MERFISH) now measures ~10,000 genes per cell, revealing RNA localization and dynamics for cell cycle analysis.

Keywords:
MERFISHRNA velocityfluorescence in situ hybridizationsingle-cell transcriptomicsspatial transcriptomics

More Related Videos

Studying Cell Cycle-regulated Gene Expression by Two Complementary Cell Synchronization Protocols
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Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Related Experiment Videos

Last Updated: Jan 19, 2026

Using an Automated Cell Counter to Simplify Gene Expression Studies: siRNA Knockdown of IL-4 Dependent Gene Expression in Namalwa Cells
10:34

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Published on: April 14, 2010

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Studying Cell Cycle-regulated Gene Expression by Two Complementary Cell Synchronization Protocols
12:02

Studying Cell Cycle-regulated Gene Expression by Two Complementary Cell Synchronization Protocols

Published on: June 6, 2017

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Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

5.4K

Area of Science:

  • Molecular Biology
  • Genomics
  • Cell Biology

Background:

  • RNA expression and spatial distribution are crucial for cellular functions.
  • Image-based transcriptomics offer insights into cellular environments.
  • Multiplexed error-robust fluorescence in situ hybridization (MERFISH) enables spatially resolved RNA quantification.

Purpose of the Study:

  • To enhance MERFISH for genome-wide RNA profiling in individual cells.
  • To investigate subcellular RNA compartmentalization.
  • To develop an in situ method for RNA velocity and cell cycle analysis.

Main Methods:

  • Increased MERFISH gene throughput to simultaneously measure ~10,000 RNA transcripts.
  • Combined MERFISH with cellular structure imaging for subcellular localization.
  • Developed an RNA velocity approach using nuclear and cytoplasmic RNA counts.

Main Results:

  • Achieved ~80% detection efficiency and ~4% misidentification rate for MERFISH.
  • Identified enrichment of specific RNA types (secretome, lncRNAs, intron-retained) in cellular compartments.
  • Inferred cell cycle states and identified ~1,600 cell cycle-dependent genes using RNA velocity.

Conclusions:

  • Enhanced MERFISH provides high-throughput, spatially resolved RNA profiling.
  • This technique reveals RNA localization patterns and dynamics.
  • It offers a powerful tool for studying gene expression, cell fate, and tissue organization.