GSE202202 Processing Pipeline

RNA-Seq code_examples 4 steps

Publication

Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis.

Nature communications (2024) — PMID 39737952

Dataset

GSE202202

RNA-seq in neurites and soma of primary hippocampal neurons isolated from P0 or P1 mice

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

    Adaptors and sequence with a quality below 20 were removed using trimmomatic (galaxy version 0.38.0)

    Trimmomatic v0.38.0
  2. 2

    Reads were aligned on mm10 genome using RNA star (galaxy version 2.7.8a+galaxy0)

  3. 3

    Number of reads per transcript was determined using FeatureCounts (galaxy version 2.0.1+galaxy2)

    featureCounts v2.0.1
  4. 4

    Differential gene expression was determined using DESeq2 (galaxy version 2.11.40.7+galaxy1)

    DESeq2 v2.11.40

Tools Used

DESeq2
Raw Source Text 
Adaptors and sequence with a quality below 20 were removed using trimmomatic (galaxy version 0.38.0)
Reads were aligned on mm10 genome using RNA star (galaxy version 2.7.8a+galaxy0)
Number of reads per transcript was determined using FeatureCounts (galaxy version 2.0.1+galaxy2)
Differential gene expression was determined using DESeq2 (galaxy version 2.11.40.7+galaxy1)
Assembly: mm10
Supplementary files format and content: Featurecounts files, reads aligned on mm10 genome
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