GSE104501
GSE GEOPoly(A) Tail Length of L4 C. elegans
Relations
Summary
Poly(A) tails are important elements in mRNA translation and stability. However, recent genome-wide studies concluded that poly(A) tail length was generally not associated with translational efficiency in non-embryonic cells. To investigate if poly(A) tail size might be coupled to gene expression in an intact organism, we used an adapted TAIL-seq protocol to measure poly(A) tails in Caenorhabditis elegans. Surprisingly, we found that well-expressed transcripts contain relatively short, well-defined tails. This attribute appears dependent on translational efficiency, as transcripts enriched for optimal codons and ribosome association had the shortest tail sizes, while non-coding RNAs retained long tails.
Overall Design
Global investigation of L4 C. elegans poly(A) tail length by using mTAIL-seq and analysis by the tailseeker2 program. Two independent biological replicates were used.
Analysis (3 steps)
View Data Processing- Base calling, trimming of adapter sequences, removal of duplicated reads and determination of poly(A) tail sizes were performed by tailseeker2.
- Reads were analyzed by mapping to the WS247 assembly of the C. elegans genome using RNA-STAR.
- Poly(A) lengths were then assigned to individual coding genes by intersecting the mapped sequences with WormBase.org WS247 gene annotations using BEDTools.
Supplementary Files (1)
GEO Samples (2)
Dataset Citations (1)
SRA Experiments (2) and Runs (2)
Total: 3907 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR6125154 | 8367234 | 2351192754 | 1647.99 | rep1_3prime.fastq.gz, rep1_5prime.fastq.gz, SRR6125154, SRR6125154.sr… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR6125155 | 11478821 | 3225548701 | 2258.51 | rep2_3prime.fastq.gz, rep2_5prime.fastq.gz, SRR6125155, SRR6125155.sr… | SRA |