Using RNA from formalin fixed paraffin embedded tissue sections for sequencing

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5 years ago

Panagiotis Karagiannis

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Using RNA from formalin fixed paraffin embedded tissue sections for sequencing

Hello there! I have some slides with mouse lung tumors and I would like to do rna sequencing. Will I be able to extract enough/good quality rna from RNA from formalin fixed paraffin embedded tissue sections for sequencing to be successful?

Experiment: RNA sequencing Mouse - Bone marrow-derived macrophages (BMDMs)

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**Dr. Susmita Sridhar** · Answer 1 · 2019-06-17T08:35:02+00:00

Generally, it should be possible, however some tissues produce much lower RNA yield. You should use an rRNA depletion protocol instead of an mRNA capture one since the RNA will probably be degraded after a capture based method. Also, try to input a higher starting amount to increase your chances of success.

**Panagiotis Karagiannis** · Answer 2 · 2019-06-20T10:55:29+00:00

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Thank you for your reply Dr. Susmita. I will repeat the experiment following your advice.

Answered 5 years ago

Panagiotis Karagiannis

**Dr. Susmita Sridhar** · Answer 3 · 2019-06-17T08:35:02+00:00

Generally, it should be possible, however some tissues produce much lower RNA yield. You should use an rRNA depletion protocol instead of an mRNA capture one since the RNA will probably be degraded after a capture based method. Also, try to input a higher starting amount to increase your chances of success.