JACUSA2 - use cases: 1 - 3

Supplementary data for use cases presented in:

RNA modification mapping with JACUSA2
Michael Piechotta, Qi Wang, Janine Altmüller, Christoph Dieterich
doi: https://doi.org/10.1101/2021.07.02.450888

Use case 1: m6A mapping by MazF

• MazF_vs_cond2_FTO_rtarrest_plain_result.out.gz (JACUSA2 output)
• Cutoff01_MazF_vs_cond2_FTO_rtarrest_plain_result.out.gz (filtered by pvalue <=0.1)
• MazF (BAM files): 
  • SRR8450805_STARmapping_uniq_rmdup.bam
  • SRR8450807_STARmapping_uniq_rmdup.bam
  • SRR8450809_STARmapping_uniq_rmdup.bam
• FTO: (BAM files):
  • SRR8450806_STARmapping_uniq_rmdup.bam
  • SRR8450808_STARmapping_uniq_rmdup.bam
  • SRR8450810_STARmapping_uniq_rmdup.bam

Use case 2: DART-seq

• APOBEC1YTH_APOBEC1YTHmut_call2_result.out.gz (JACUSA2 output)
• APOBEC1YTH (BAM files):
  • SRR9940470_STARmapping_uniq_rmdup.bam
  • SRR9940471_STARmapping_uniq_rmdup.bam
  • SRR9940472_STARmapping_uniq_rmdup.bam
• APOBEC1YTHmut (BAM files):
  • SRR9940474_STARmapping_uniq_rmdup.bam
  • SRR9940475_STARmapping_uniq_rmdup.bam
  • SRR9940476_STARmapping_uniq_rmdup.bam

Use case 3: Nanopore

• WT_vs_KO_call2_result.out.gz & WT100_vs_WT0_call2_result.out.gz (JACUSA2 output)
• WT (BAM files):
  • HEK293T-WT-rep2.bam
  • HEK293T-WT-rep3.bam
  • HEK293T-WT-100-rep1.bam
  • HEK293T-WT-100-rep2.bam
  • HEK293T-WT-100-rep3.bam
• KO (BAM files):
  • HEK293T-KO-rep2.bam
  • HEK293T-KO-rep3.bam
  • HEK293T-WT-0-rep1.bam
  • HEK293T-WT-0-rep2.bam

[1] Zhang, Z., Chen, L.-Q., Zhao, Y.-L., Yang, C.-G., Roundtree, I.A., Zhang, Z., Ren, J., Xie, W., He, C., Luo, G.-Z.: Single-base mapping of m6a by an antibody-independent method. Science advances 5, 0250 (2019). doi:10.1126/sciadv.aax0250

[2] Garcia-Campos, M.A., Edelheit, S., Toth, U., Safra, M., Shachar, R., Viukov, S., Winkler, R., Nir, R., Lasman, L., Brandis, A., Hanna, J.H., Rossmanith, W., Schwartz, S.: Deciphering the ”m6a code” via antibody-independent quantitative profiling. Cell 178, 731–74716 (2019). doi:10.1016/j.cell.2019.06.013

[3] Meyer, K.D.: Dart-seq: an antibody-free method for global m6a detection. Nature methods 16, 1275–1280 (2019). doi:10.1038/s41592-019- 0570-0

[4] Pratanwanich, P.N., Yao, F., Chen, Y., Koh, C.W.Q., Hendra, C., Poon, P., Goh, Y.T., Yap, P.M.L., Yuan, C.J., Chng, 6 made available under aCC-BY-NC-ND 4.0 International license. (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is bioRxiv preprint doi: https://doi.org/10.1101/2021.07.02.450888; this version posted July 4, 2021. The copyright holder for this preprint W.J., Ng, S., Thiery, A., Goh, W.S.S., G¨oke, J.: Detection of differential rna modifications from direct rna sequencing of human cell lines. bioRxiv (2020). doi:10.1101/2020.06.18.160010. https://www.biorxiv.org/content/early/2020/06/20/2020.06.18.160010.full.pdf