GSE36648 Processing Pipeline

GSE code_examples 1 step

Publication

Evidence for premature aging due to oxidative stress in iPSCs from Cockayne syndrome.

Human molecular genetics (2012) — PMID 22661500

Dataset

GSE36648

Expression data in induced pluripotent stem cells (iPSCs) derived from a DNA repair deficient fibroblast

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

    HuGene-1.0-st were analyzed by using affymetrix power tools (apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d ../../Human/CD_HG-U133_Pl us_2_Libfiles/HG-U133_Plus_2.cdf -o gene-level-output CM0811101A.CEL CM0811101B.CEL CM0811101C.CEL CM0811102A.CEL CM08111 02B.CEL CM0811102C.CEL CM081110CA.CEL CM081110CB.CEL CM081110CC.CEL CM081110HA.CEL CM081110HB.CEL CM081110HC.CEL CM081110 RA.CEL CM081110RB.CEL CM081110RC.CEL )

    Microarray vNot specified
    $ Bash example 
    # Affymetrix Power Tools (APT) is proprietary software.
# Download and install from Thermo Fisher Scientific website:
# https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-data-analysis/affymetrix-power-tools.html

# The HG-U133_Plus_2.cdf file is a Chip Definition File for the Affymetrix Human Genome U133 Plus 2.0 Array.
# It is typically obtained from Thermo Fisher Scientific (formerly Affymetrix) and should be placed in the specified path.
# Example (illustrative, actual download may vary):
# mkdir -p ../../Human/CD_HG-U133_Plus_2_Libfiles/
# wget -O ../../Human/CD_HG-U133_Plus_2_Libfiles/HG-U133_Plus_2.cdf "https://assets.thermofisher.com/TFS-Assets/LSG/support-files/HG-U133_Plus_2.cdf"

apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d ../../Human/CD_HG-U133_Plus_2_Libfiles/HG-U133_Plus_2.cdf -o gene-level-output CM0811101A.CEL CM0811101B.CEL CM0811101C.CEL CM0811102A.CEL CM0811102B.CEL CM0811102C.CEL CM081110CA.CEL CM081110CB.CEL CM081110CC.CEL CM081110HA.CEL CM081110HB.CEL CM081110HC.CEL CM081110RA.CEL CM081110RB.CEL CM081110RC.CEL

Tools Used

Microarray
Raw Source Text 
HuGene-1.0-st were analyzed by using affymetrix power tools (apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d ../../Human/CD_HG-U133_Pl  us_2_Libfiles/HG-U133_Plus_2.cdf -o gene-level-output CM0811101A.CEL CM0811101B.CEL CM0811101C.CEL CM0811102A.CEL CM08111  02B.CEL CM0811102C.CEL CM081110CA.CEL CM081110CB.CEL CM081110CC.CEL CM081110HA.CEL CM081110HB.CEL CM081110HC.CEL CM081110  RA.CEL CM081110RB.CEL CM081110RC.CEL )
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