GSE86223 Processing Pipeline

GSE code_examples 6 steps

Publication

Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

Neuron (2016) — PMID 27773581

Dataset

GSE86223

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_…

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

    Cel files were analyzed using Expression Console (build 1.4.1.46, Affymetrix), with RMA normalization and DABG probe-level detection.

    Microarray
  2. 2

    Only probesets with detection p-value ≤ 0.05 in more than half of the microarray samples were considered for downstream analysis.

    Microarray
  3. 3

    All probes corresponding to cassette exons profiled on the microarray (comprising exclusion junction, upstream and downstream inclusion junction, and inclusion exonic probes) were identified and normalized against the average signal on a per-gene basis to remove gene expression changes.

    Microarray
  4. 4

    Student’s t-test was performed on residuals for inclusion probes and exclusion probes separately to identify robust splicing changes, which were quantified by SepScore ( defined as the normalized change in exclusion minus the normalized change in inclusion).

  5. 5

    HTA-2_0.r1.pgf

  6. 6

    HTA-2_0.r1.Psrs.mps

Tools Used

Microarray
Raw Source Text 
Cel files were analyzed using Expression Console (build 1.4.1.46, Affymetrix), with RMA normalization and DABG probe-level detection. Only probesets with detection p-value ≤ 0.05 in more than half of the microarray samples were considered for downstream analysis. All probes corresponding to cassette exons profiled on the microarray (comprising exclusion junction, upstream and downstream inclusion junction, and inclusion exonic probes) were identified and normalized against the average signal on a per-gene basis to remove gene expression changes. Student’s t-test was performed on residuals for inclusion probes and exclusion probes separately to identify robust splicing changes, which were quantified by SepScore ( defined as the normalized change in exclusion minus the normalized change in inclusion).
HTA-2_0.r1.pgf
HTA-2_0.r1.Psrs.mps
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