update c29

prepare/prepare-29.qmd

@@ -16,3 +16,7 @@ Choquet K, Baxter-Koenigs AR, Dülk SL, Smalec BM, Rouskin S, Churchman LS. **Pr
 Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. **The complete sequence of a human genome.** Science. 2022  PMID: 35357919; PMCID: PMC9186530. [[Link]](https://pubmed.ncbi.nlm.nih.gov/35357919/)
 
 Stergachis AB, Debo BM, Haugen E, Churchman LS, Stamatoyannopoulos JA. **Single-molecule regulatory architectures captured by chromatin fiber sequencing.** Science. 2020 Jun 26;368(6498):1449-1454. doi: 10.1126/science.aaz1646. PMID: 32587015.
+
+### Nanopore protein sequencing
+
+Motone K, Kontogiorgos-Heintz D, Wee J, Kurihara K, Yang S, Roote G, Fox OE, Fang Y, Queen M, Tolhurst M, Cardozo N, Jain M, Nivala J. Multi-pass, single-molecule nanopore reading of long protein strands. Nature. 2024 Sep;633(8030):662-669. doi: 10.1038/s41586-024-07935-7. Epub 2024 Sep 11. PMID: 39261738; PMCID: PMC11410661.

slides/slides-29.qmd

@@ -3,18 +3,6 @@ title: "Long-read sequencing platforms & applications"
 author: "Jay Hesselberth"
 ---
 
-## Business
-
-- No homework this weekend.
-- Single-cell mRNA-seq next week. 1 problem set.
-- Final project presentations.
-
-  * Would like to complete in 1 day. 5-7 minutes each.
-  * Make Google Slides and send us a link.
-  * How many groups?
-
-- Survey at the end. Please fill it out, we want and need your feedback.
-
 ## Short & long read DNA sequencing {.smaller}
 
 ::: {layout-ncol=2 .nostretch}
@@ -23,8 +11,7 @@ author: "Jay Hesselberth"
 ![for the trees](../img/block-rna/birds-eye.jpg)
 :::
 
-We have entered a new era (sorry, Swifties) wherein routine application of long-read sequencing is revealing new principles of gene regulation.
-
+We have entered a new era (Swifties unite) wherein routine application of long-read sequencing is revealing new principles of gene regulation.
 
 ## Comparing data from short- and long-read experiments {.smaller}
 
@@ -112,19 +99,12 @@ Stergachis et al. (2020) Nature
 Alfonso-Gonzalez et al. (2023) Cell
 :::
 
-## Applications beyond long-read sequencing {.smaller}
-
-The nanopore sequencing technology has been adapted for more than DNA sequencing. For example,
-we can now analyze modifications on tRNA, where the modifiations leave unique signatures in 
-the current traces.
-
-::: {layout-ncol=2}
-
-![](../img/block-rna/trna-seq.png)
-
-![](../img/block-rna/aa-tRNA-sequencing.png)
-
-:::
+## Applications beyond long-read nucleic acid sequencing {.smaller}
 
+We might be able to sequence proteins soon. Why is this cool?
 
+![](../img/block-rna/nanopore-protein.jpg){fig-align="center"}
 
+::: aside
+Motone et al (2024) Nature
+:::