Total RNA of 2-3 clones of each cell line (Control and OCT4A overexpression) was extracted with the RNeasy kit (Qiagen), following the manufacturer's protocol. Gene expression profiling were carried out independently for each sample using Affymetrix GeneChip® Human Gene 2.0 ST whole-transcript arrays (Affymetrix, Santa Clara, CA, USA). The quality control and normalization of data were processed by Affymetrix® Expression Console Software (Affymetrix). Differentially expressed genes were identified with the One-Way ANOVA, with a p-value cutoff of 0.05, using Transcriptome Analysis Console v3.0 (Affymetrix). Functional Annotation was conducted on Ingenuity Pathway Analysis (Qiagen). Raw data is available at GEO with accession number: GSE77947.
Genechip human gene 2.0 st whole transcript arrays
Manufactured by Thermo Fisher Scientific
Sourced in United States
The GeneChip® Human Gene 2.0 ST whole-transcript arrays are designed for gene expression analysis. The arrays provide comprehensive coverage of the human transcriptome, enabling the measurement of all protein-coding transcripts and known non-coding transcripts.
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Lab products found in correlation
Rneasy kit, by Qiagen (1 mentions)
Ingenuity pathway analysis (ipa), by Qiagen (1 mentions)
Transcriptome analysis console v3, by Thermo Fisher Scientific (1 mentions)
Affymetrix expression console software, by Thermo Fisher Scientific (1 mentions)
Hiseq sequencer, by Illumina (1 mentions)
Transcriptome analysis console, by Thermo Fisher Scientific (1 mentions)
Trueseq kits, by Illumina (1 mentions)
60k whole genome platform, by Agilent Technologies (1 mentions)
2 protocols using genechip human gene 2.0 st whole transcript arrays
1
Transcriptomic Profiling of OCT4A Overexpression
2
Genome-wide Expression and Variation Analysis
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Gene expression profiling was determined with Affymetrix GeneChip Human Gene 2.0 ST whole-transcript arrays (GEO accession number: GSE103935). Identification (12) and interactome analysis of differentially expressed genes were performed with Transcriptome Analysis Console (Affymetrix) and IPA Software (Ingenuity Pathway Analysis, Qiagen), respectively. Wholeexome sequencing was performed using Illumina's TrueSeq kits and the Illumina HiSeq sequencer. Candidate pathogenic mutations were determined by allele frequency < 0.05 in NIH 1000 Genomes Project and by SIFT and FATHMM algorithms. Array comparative genomic hybridization was performed using 60K whole-genome platform (Agilent Technologies) following the manufacturer's recommendation. Detailed description is provided in Supplementary Experimental Procedures.
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