RNA from three independent SPINK1 KD experiments with nontarget controls
and from three independent IL-6 KD experiments with nontarget controls were
extracted using TRIzol (Invitrogen) and evaluated for differences in gene
expression using the Affymetrix human transcriptome Array v2.0. Results were
analyzed using GeneSpring 14.9.1 (Agilent), as described previously [53 , 54 (link)]. Briefly, data were processed using GCRMA and filtered to remove
entities (transcripts) with raw data values below 50 in more than 75% of the
samples, and moderated t-tests were used to identify differentially expressed
entities when comparing knockdown samples (combining all JHOC9 and JHOC5
knockdown samples) vs controls (combining all JHOC9 and JHOC5 nontarget control
samples) which were mapped to genes and compared as genesets to publically
available databases using Illumina Correlation Engine. Gene expression profiles
have been deposited in the Gene Expression Omnibus (GSE140179).
and from three independent IL-6 KD experiments with nontarget controls were
extracted using TRIzol (Invitrogen) and evaluated for differences in gene
expression using the Affymetrix human transcriptome Array v2.0. Results were
analyzed using GeneSpring 14.9.1 (Agilent), as described previously [53 , 54 (link)]. Briefly, data were processed using GCRMA and filtered to remove
entities (transcripts) with raw data values below 50 in more than 75% of the
samples, and moderated t-tests were used to identify differentially expressed
entities when comparing knockdown samples (combining all JHOC9 and JHOC5
knockdown samples) vs controls (combining all JHOC9 and JHOC5 nontarget control
samples) which were mapped to genes and compared as genesets to publically
available databases using Illumina Correlation Engine. Gene expression profiles
have been deposited in the Gene Expression Omnibus (GSE140179).
