Transcriptomic Analysis of Rnq1 Loss and Prionization: Effects on Translation Pathways and Energy Metabolism

Description

Prion proteins can undergo self-perpetuating conformational changes that alter their functions. One such protein, Rnq1, is unknown for its physiological functions. We conducted RNA-seq experiments to compare the effects of Rnq1 depletion and prionization. This dataset includes summary of the sequencing data, especially information on differentially expressed genes (DEGs).

Description of the data/file structure

The three supplemental tables have similar data structues, containing summarized RNA-seq results generated with a standard pipeline. These files are in .CVS format and can be opened with Excel or similar software. Table S1_RM vs WT is for DEGs between Rnq1 depletion and wildtype non-prion strains; Table S2_RP vs WT is for DEGs between Rnq1 prion and wildtype strains; Table S3_RP vs RM is for Rnq1 prion and depletion strains. 

• Systematic Name: Yeast systematic gene name
• Standard Name: Standard gene name
• Allias: other name
• Chr: chromosome
• Start: gene start position
• End: gene end position 
• width: Gene size in base pairs
• Strand: forward or complementary strand
• LL.RM1: Rnq1 depletion mutant sample 1
• LL.RM2: Rnq1 depletion mutant sample 2
• LL.RM3: Rnq1 depletion mutant sample 3
• RP1: Rnq1 prion sample 1
• RP2: Rnq1 prion sample 2
• RP3: Rnq1 prion sample 3
• LL.CK1: wildtype non-prion sample 1
• LL.CK2: wildtype non-prion sample 2
• LL.CK3: wildtype non-prion sample 3
• meanRM: average reads of Rnq1 depletion mutant samples
• meanRP: average reads of Rnq1 prion samples
• meanWT: average reads of Wildtype non-prion samples
• FC: fold change
• logFC: log(fold change)
• log(adjP)abs: log value of adjusted P
• meanALL: average of all
• STDEVall: STDEV
• logCPM: log value of count per million
• LR: system value from the pipeline 
• PValue: P value
• adj.p: adjusted P value
• up: upregulated based on the cutoff criteria
• dn: downregulated based on the cutoff criteria
• biotype: Feature type of gene
• description: gene function description

Additional details