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--- blastocystis_orf160 [2025/11/10 15:11] – [Little to no expression of orf160 in regular and riboZeroPlus RNAseq data of ST7C] 134.190.191.148
+++ blastocystis_orf160 [2025/11/10 15:20] (current) – [Little to no expression of orf160 in regular and riboZeroPlus RNAseq data of ST7C] 134.190.191.148
@@ Line 421: / Line 421: @@
 A lot of reads still mapped to the rRNA genes, but all the other areas still had more than sufficient enough coverage as well.
-Importantly, the mitochondrial genome had much more reads mapping to it:
+Importantly, **the mitochondrial genome had much more reads mapping to it**:
 {{:overall_mro_expression_ribozero.png|}}
-This is not just the result of a higher throughput. The throughput of the riboZeroPlus run (179 506 076 mapped reads) was about twice that of the original RNAseq run (85 875 153 reads), but far more than twice time the amount of reads now mapped to the MRO genome. (NOTE that for both IGV figures I used the same coverage scale of 2000 in the Coverage track).
+**This is not just the result of a higher throughput**. The throughput of the riboZeroPlus run (179 506 076 mapped reads) was about twice that of the original RNAseq run (85 875 153 reads), but far more than twice time the amount of reads now mapped to the MRO genome. (NOTE that for both IGV figures I used the same coverage scale of 2000 in the Coverage track).
 What is striking is that the mitochondrial rRNA genes still had an enormous amount of coverage. Perhaps next time you want to sequence the mitochondrial transcriptome of some organism, also include probes targeting the mitochondrial rRNA genes!
+Another striking thing is that it seems that **RNAseq coverage of mitochondrial ribosomal genes is much lower** than that of the //nad// genes! Exceptions seem to be //rps12// and //rpl16//.
+Zooming in to //orf160// / //rpl10//:
+{{:orf160_expression_screenshot.png|}}
+Unfortunately again it seems we are not seeing any significant evidence of expression of this gene. It may be that the throughput for this gene in particular was not high enough to detect any real expression, so we can't rule it out. Any reads that are overlapping with orf160 may be 3'UTR reads from the //nad7// gene upstream (here annotated as NdhH)
 ====== Ideas to explore ======