Update RNA-seq materials

[sjspielman]

Closes #901
Closes #798
Closes #911

This PR updates RNA-seq materials; opening as draft until all the bioc 3.22 changes go in to confirm we're all set for #911.

A couple changes here:

• Two changes for [this comment https://github.com/2024 August issues: Pathway and bulk materials #798#issuecomment-2302078403]: fix a typo in which QC report we show, and update the link since the relevant "note" is actually a section up in the salmon docs
• For Fix typo in 01-qc_trim_quant.Rmd #901, fix another typo where we pointed to the wrong sample id
• For this comment save the modified data frame to a new variable to reduce odds of bugs during instruction