Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-FLAG M2 affinity gel | Sigma-Aldrich | A2220 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 3X FLAG peptide | Sigma-Aldrich | F4799 |
| T4 RNA Ligase 2, truncated K227Q | New England Biolabs | M0351S |
| TURBO DNA-free Kit | Thermo Fisher Scientific | AM1907 |
| T4 PNK | New England Biolabs | M0201S |
| Superscript III First-strand Synthesis System | Thermo Fisher Scientific | 18080051 |
| RNaseOUT Recombinant Ribonuclease Inhibitor | Thermo Fisher Scientific | 10777109 |
| Proteinase K | Sigma-Aldrich | P6556 |
| Pierce Protease Inhibitor Tablets, EDTA-free | Thermo Fisher Scientific | 88266 |
| Critical Commercial Assays | ||
| PolyATtract® mRNA Isolation System | Promega | Z5300 |
| NEBNext Ultra Directional RNA Library Prep Kit for Illumina | New England Biolabs | E7420S |
| RNA 6000 Pico Kit | Agilent | 5067–1513 |
| High Sensitivity DNA Kit | Agilent | 5067–4626 |
| Deposited Data | ||
| RNA-seq data | GSE168814 | |
| Experimental Models: Organisms/Strains | ||
| C. neoformans: GPATCH1-CBP-2XFLAG | This Study | CM2047 |
| C. neoformans: RBM17-CBP-2XFLAG | This Study | CM2046 |
| C. neoformans: RBM5-CBP-2XFLAG | This Study | CM2048 |
| C. neoformans: untagged | Madhani Laboratory | CM025 |
| C. neoformans: cnag_05579Δ:: NEO | Madhani Laboratory | CK5778 |
| C. neoformans: cnag_00761Δ:: NEO | Madhani Laboratory | CK3285 |
| C. neoformans: cnag_00294Δ:: NEO | Madhani Laboratory | CK1844 |
| C. neoformans: cnag_03665Δ:: NEO | Madhani Laboratory | CK2692 |
| C. neoformans: cnag_02401Δ:: NEO | Madhani Laboratory | CK1446 |
| C. neoformans: cnag_04679Δ:: NEO | Madhani Laboratory | CK5311 |
| C. neoformans: cnag_02260Δ:: NEO | Madhani Laboratory | CK4072 |
| C. neoformans: cnag_05845Δ:: NEO | Madhani Laboratory | CK5920 |
| C. neoformans: cnag_06616Δ:: NEO | Madhani Laboratory | CK954 |
| C. neoformans: cnag_05030Δ:: NEO | Madhani Laboratory | CK5488 |
| C. neoformans: cnag_01058Δ:: NEO | Madhani Laboratory | CK3448 |
| C. neoformans: cnag_02340Δ:: NEO | Madhani Laboratory | CK4114 |
| C. neoformans: cnag_05307Δ:: NEO | Madhani Laboratory | CK5607 |
| C. neoformans: cnag_02773Δ:: NEO | Madhani Laboratory | CM |
| C. neoformans: cnag_03031Δ:: NEO | Madhani Laboratory | CK4458 |
| Software and Algorithms | ||
| Samtools | 38 | http://samtools.sourceforge.net/ |
| SciPy | 39 | https://github.com/scipy/scipy |
| Cutadapt | N/A | https://github.com/marcelm/cutadapt |
| FastX toolkit | N/A | http://hannonlab.cshl.edu/fastx_toolkit |
| HTSeq | 40 | https://pypi.python.org/pypi/HTSeq |
| BEDTools | N/A | https://github.com/arq5x/bedtools2 |
| Integrative Genomics Viewer | 41 | http://software.broadinstitute.org/software/igv/ |
| BAS: Bayesian Variable Selection and Model Averaging using Bayesian Adaptive Sampling (R) | 42 | https://cran.r-project.org/web/packages/BAS/index.html |
| Pandas (version 1.1.1) | 43 | https://zenodo.org/record/4067057#.X7RG3NNKi34 |
| SP Pipeline | 15 | https://github.com/jeburke/SPTools/ |
| IP2 | N/A | http://www.integratedproteomics.com |
| RawConverter | 44 | http://fields.scripps.edu/rawconv/ |
| ProLucid | 45 | http://fields.scripps.edu/downloads.php |
| DTASelect | 46 | http://fields.scripps.edu/yates/wp/ |
| Census 2 | 47 | http://fields.scripps.edu/census/ |
| STAR | 37 | https://github.com/alexdobin/STAR |
| Matplotlib (version 3.3.3) | 48 | https://matplotlib.org/ |
| Numpy | 49 | https://numpy.org |
| Seqlogo | 50 | https://github.com/betteridiot/seqlogo |
| Statsmodels (version 0.13.0) | 51 | https://www.statsmodels.org/dev/index.html |
| Statannot | 52 | https://github.com/webermarcolivier/statannot |
| Pybedtools | 53 | https://daler.github.io/pybedtools/ |
| JUM (version 2.0.2) | 18 | https://github.com/qqwang-berkeley/JUM |