GSE222216 Processing Pipeline

RNA-Seq code_examples 4 steps

Publication

Remodeling oncogenic transcriptomes by small molecules targeting NONO.

Nature chemical biology (2023) — PMID 36864190

Dataset

GSE222216

Transcriptome changes in 22Rv1 cells with a double knockout or over expression of C145S, Empty vector, or Wild type NONO.

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

    Transcript abundance was quantified using Salmon [v1.3.0] with GENCODE v37 annotation.

    Salmon v1.3.0
  2. 2

    Gene level quantification was performed using tximeta [v1.8.4].

  3. 3

    Differential gene expression was analyzed by DESeq2 [v1.30.1]

    DESeq2 v1.30.1
  4. 4

    processed data files format and content: gene counts

Tools Used

DESeq2
Raw Source Text 
Transcript abundance was quantified using Salmon [v1.3.0] with GENCODE v37 annotation.
Gene level quantification was performed using tximeta [v1.8.4].
Differential gene expression was analyzed by DESeq2 [v1.30.1]
genome build: HG19
processed data files format and content: gene counts
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