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| Status |
Public on May 31, 2023 |
| Title |
Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay [Ribo-seq] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Other
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| Summary |
Cytoplasmic poly(A)-binding protein (PABPC, yeast Pab1) is involved in various stages of mRNA post-transcriptional control, including translation initiation, translation termination, and mRNA decay regulation. Due to the multi-functional properties of PABPC, attempts to define a specific role for PABPC in vivo by deleting, depleting, overexpressing, or mutating the protein has led to conflicting models of PABPC's function. To specifically assess direct and indirect consequences of deleting PABPC, we generated and analyzed RNA-Seq, ribosome profiling, and mass spectrometry data from yeast cells lacking Pab1.
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| Overall design |
RNA-Seq and ribosome profiling of WT, pbp1∆, and pab1∆pbp1∆ cells (pbp1∆ is needed to suppress lethality of pab1∆), 3 replicates for each strain.
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| Contributor(s) |
Mangkalaphiban K, Jacobson A |
| Citation(s) |
37398227 |
| BioProject |
PRJNA952648 |
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| Submission date |
Apr 13, 2023 |
| Last update date |
Sep 11, 2023 |
| Contact name |
Kotchaphorn Mangkalaphiban |
| E-mail(s) |
kotchaphorn.mangkalaphiban@umassmed.edu
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| Organization name |
University of Massachusetts Medical School
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| Lab |
Jacobson Lab
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| Street address |
368 Plantation St.
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| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platforms (2) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
| GPL26302 |
NextSeq 550 (Saccharomyces cerevisiae) |
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| Samples (9)
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| GSM7173313 |
Yeast W303, pbp1 deletion, replicate 1 |
| GSM7173314 |
Yeast W303, pbp1 deletion, replicate 2 |
| GSM7173315 |
Yeast W303, pbp1 deletion, replicate 3 |
| GSM7173316 |
Yeast W303, pab1 and pbp1 deletions, replicate 1 |
| GSM7173317 |
Yeast W303, pab1 and pbp1 deletions, replicate 2 |
| GSM7173318 |
Yeast W303, pab1 and pbp1 deletions, replicate 3 |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE229692_RAW.tar |
22.8 Mb |
(http)(custom) |
TAR (of WIG) |
| GSE229692_pab1_strains_RPF_RSEM_FPKM_genes.results.csv.gz |
153.5 Kb |
(ftp)(http) |
CSV |
| GSE229692_pab1_strains_RPF_RSEM_FPKM_isoforms.results.csv.gz |
156.4 Kb |
(ftp)(http) |
CSV |
| GSE229692_pab1_strains_RPF_RSEM_expected_count_genes.results.csv.gz |
167.8 Kb |
(ftp)(http) |
CSV |
| GSE229692_pab1_strains_RPF_RSEM_expected_count_isoforms.results.csv.gz |
171.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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