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CRISPR and crRNAs

CRISPR and crRNAs

Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...

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Updated: Dec 18, 2025

Efficient Generation of hiPSC Neural Lineage Specific Knockin Reporters Using the CRISPR/Cas9 and Cas9 Double Nickase System

Efficient Generation of hiPSC Neural Lineage Specific Knockin Reporters Using the CRISPR/Cas9 and Cas9 Double Nickase System

Published on: May 28, 2015

Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data.

Hamim Zafar^1,2,3, Chieh Lin⁴, Ziv Bar-Joseph^5,6

¹Department of Computer Science and Engineering, Indian Institute of Technology Kanpur, Kanpur, India.

Nature Communications

|June 18, 2020

Summary

This summary is machine-generated.

We developed LinTIMaT, a new statistical method for reconstructing cell lineages using both mutation and expression data. This approach overcomes computational challenges, enabling more accurate and integrated developmental lineage trees.

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Generation of Defined Genomic Modifications Using CRISPR-CAS9 in Human Pluripotent Stem Cells

Generation of Defined Genomic Modifications Using CRISPR-CAS9 in Human Pluripotent Stem Cells

Published on: September 25, 2019

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Last Updated: Dec 18, 2025

Efficient Generation of hiPSC Neural Lineage Specific Knockin Reporters Using the CRISPR/Cas9 and Cas9 Double Nickase System

Efficient Generation of hiPSC Neural Lineage Specific Knockin Reporters Using the CRISPR/Cas9 and Cas9 Double Nickase System

Published on: May 28, 2015

Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers MADM

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Generation of Defined Genomic Modifications Using CRISPR-CAS9 in Human Pluripotent Stem Cells

Generation of Defined Genomic Modifications Using CRISPR-CAS9 in Human Pluripotent Stem Cells

Published on: September 25, 2019

Area of Science:

Developmental Biology
Computational Biology
Genomics

Background:

Single-cell RNA sequencing and CRISPR-Cas9 barcode editing are used to study developmental lineages.
Existing methods face computational challenges due to noisy mutation data and inability to combine experiments.

Purpose of the Study:

To develop a novel statistical method for reconstructing cell lineages.
To integrate mutation and expression data for improved lineage inference.
To enable the reconstruction of species-invariant lineage trees.

Main Methods:

Developed LinTIMaT, a maximum-likelihood statistical framework.
Integrated single-cell RNA sequencing (expression) data with CRISPR-Cas9 barcode editing (mutation) data.
Applied the method to reconstruct cell lineages at the whole organism level.

Main Results:

LinTIMaT resolves ambiguities present in mutation-only lineage inference using expression data.
Expression data enables the integration of multiple experimental lineages into a single, invariant lineage tree.
Reconstructed lineages show improved cell type coherence and functional gene set significance.

Conclusions:

LinTIMaT offers a robust method for accurate cell lineage reconstruction.
The method provides new insights into progenitor populations and differentiation pathways.
Integrating mutation and expression data is crucial for advancing developmental lineage studies.