GSE160397
Mar1 deletion and RNA enrichment in Cryptococcus neoformans: pilot data for a high-throughput sequencing course
Mar1 deletion and RNA enrichment in Cryptococcus neoformans: pilot data for a high-throughput sequencing course. The goal of this project was to generate pilot data in preparation for a summer course on high-throughput sequencing where participants prepared their own RNA-Seq libraries and analyzed the resulting data. This pilot experiment addressed two questions: 1. Does this experimental system (Cryptococcus neoformans H99 wildtype and mar1 deletion mutant grown in YPD and tissue culture media) provide a good dataset for course participants to analyze. 2. Which rRNA depletion method is best to use in the wetlab component of the course. This data was generated in preparation for the intensive summer course on high-throughput sequencing, funded by NIH grant 5R25EB023928-03 "A hands-on, integrative next-generation sequencing course: design, experiment, and analysis". Overall design: This project generated 63 libraries from 24 different samples. Samples from 6 biological replicates were generated for each treatment x genotype. The two treatments conditions were growth in YPD and tissue culture media. The two genotypes were H99 wildtype and mar1 deletion mutant. Two libraries were made from each RNA sample using different methods for rRNA depletion: poly(A) isolation and Ribo-Zero. For 3 of the samples libraries were also made from unenriched RNA and RNA enriched using the RNase H method. For these 3 samples unenriched, RNase H, and poly(A) enriched libraries were prepared and sequenced in 2019 and unenriched, poly(A), and Ribo-Zero libraries were prepared and sequenced in 2018. All other libraries were prepared and sequenced in 2018.