why there are read counts in the gene knock out rat RNA-seq data

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Yijing • 0

@0fcbf96d

Last seen 20 months ago

Germany

Hi,

I am analyzing transcriptomic data for gene knock out rats. I wonder why there are still read counts in the knock out rat?

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ReadCounts • 1.8k views

ADD COMMENT • link 2.0 years ago Yijing • 0

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How was the gene knocked out? If they just introduced a stop codon into it, transcription could still happen.

ADD REPLY • link 2.0 years ago swbarnes2 ★ 1.4k

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Even for a multi-exon knockout you could (and indeed we often do in our KO mice) still detect some borderline expression. I mean, look at your data, you have a strong reduction of reads, almost two powers of 10, so that is fine. After all it's the functional protein knockout that counts, anyway the RNA-seq counts will be highly significant.

ADD REPLY • link 2.0 years ago ATpoint ★ 4.5k

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Yes, it is evident that the gene's expression is reduced. But I just want to figure out why there are still some counts? It is due to the knock out technology or RNA-seq technology?

ADD REPLY • link 2.0 years ago Yijing • 0

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The gene was totally knockedout by CRISPR/cas9. enter image description here

ADD REPLY • link 2.0 years ago Yijing • 0

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