GSE280897 RNA-seq Data Processing

RNA-seq geo_data_processing 6 steps

Publication

Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.

Cancer research (2025) — PMID 41411621

Dataset

GSE280897

PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [RNA-seq]

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

Reads were mapped using STAR 2.7.6a

STAR v2.7.6a
2

Read count extraction was performed using featureCounts from the Subread package.

featureCounts
3

Results were sorted into counts matrices
4

TPM was calculated manually from counts matrix
5

Differential splicing analysis was performed on STAR-aligned reads using rMATS 4.0.2.

STAR
6

For each condition, shRNA knockdown samples represent SAMPLE_1, while non-targeting controls (shNT1, shNT2, and shNT3) represent SAMPLE_2.

Tools Used

STAR STAR

Raw Source Text

Reads were mapped using STAR 2.7.6a
Read count extraction was performed using featureCounts from the Subread package. Results were sorted into counts matrices
TPM was calculated manually from counts matrix
Differential splicing analysis was performed on STAR-aligned reads using rMATS 4.0.2. For each condition, shRNA knockdown samples represent SAMPLE_1, while non-targeting controls (shNT1, shNT2, and shNT3) represent SAMPLE_2.
Assembly: Assembly: GRCh38
Supplementary files format and content: Supplementary files format and content: csv files include TPM values for each sample in comparison to non-targeting shRNA control, along with sample means and standard deviations
Supplementary files format and content: Supplementary files format and content: tab-delimited text files include differential skipped exon splicing analysis for each knockdown (SE.MATS.JC.txt from rMATS)

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