GSE230349 Processing Pipeline

OTHER code_examples 8 steps

Publication

Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery.

Nucleic acids research (2023) — PMID 37739431

Dataset

GSE230349

Seryl-tRNA synthetase promotes translational readthrough via mRNA binding by involving the selenocysteine incorporation machinery

Warning: Pipeline descriptions and code snippets may be inferred or AI-generated. Use them only as a starting point to guide analysis, and validate before use.

Processing Steps

Generate Jupyter Notebook
  1. 1

    Ribosomal footprints were analyzed as described by Ingolia et al. with these modifications: Trimgalore was used to trim off adapters and clip the first nucleotide off the 5’ end.

    Trim Galore
  2. 2

    Reads were then mapped to ribosomal RNA using bowtie2 (39) and unmapped reads were further mapped to the human transcriptome (v19) with STAR aligner (33).

    STAR GitHub
  3. 3

    Expected read length distribution was tested with the R package RiboProfiling.

    R
  4. 4

    To center ribosomes and obtain a list of genes with P-sites in their 3’ UTR, we used functionalities within Ribowaltz (40) and a custom python script by Scott Adamson, UConn, and Jax Laboratories.

    Python
  5. 5

    Observed/expected ratios were calculated using a custom script by Scott Adamson.

  6. 6

    Obs/exp indicates the number of observed codons in the A-site of the ribosome vs the calculated hypothetical expected number of observations.

  7. 7

    If ribosome pausing occurs, obs/exp > 1.

  8. 8

    Library strategy: Ribo-Seq

    Ribo-seq

Tools Used

Trim Galore STAR R Python Ribo-seq
Raw Source Text 
Ribosomal footprints were analyzed as described by Ingolia et al. with these modifications: Trimgalore was used to trim off adapters and clip the first nucleotide off the 5’ end. Reads were then mapped to ribosomal RNA using bowtie2 (39) and unmapped reads were further mapped to the human transcriptome (v19) with STAR aligner (33).
Expected read length distribution was tested with the R package RiboProfiling. To center ribosomes and obtain a list of genes with P-sites in their 3’ UTR, we used functionalities within Ribowaltz (40) and a custom python script by Scott Adamson, UConn, and Jax Laboratories.
Observed/expected ratios were calculated using a custom script by Scott Adamson. Obs/exp indicates the number of observed codons in the A-site of the ribosome vs the calculated hypothetical expected number of observations. If ribosome pausing occurs, obs/exp > 1.
Assembly: hg19
Supplementary files format and content: Excel file
Library strategy: Ribo-Seq
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