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Figure 4 | BMC Genomics

Figure 4

From: Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha

Figure 4

Analysis of gene expression changes upon ZNF217 knockdown in MCF7 cells. (A) A scatterplot of expression data from RNA-seq experiments. Each point corresponds to one NCBI Reference Sequence (RefSeq) transcript with fragments per kilobase of exon model per million mapped reads (FPKM) values for control and ZNF217 knockdown samples shown on an exponential scale. Significantly affected transcripts (FDR < 0.05 with a 1.25-fold change cuttoff) are depicted (red upregulated and blue downregulated upon ZNF217 knockdown). The dashed line represents no change in gene expression between the two samples. (B) The triplicate biological (sequenced) RNA samples from siScrambled- or siZNF217- treated MCF7 cells were analyzed by quantitative RT-PCR. ABI expression assay Taqman probes to measure transcript levels of six genes are indicated. Each sample was assayed in triplicate and the cT values were normalized to GAPDH. Average relative transcript level was graphed using BioRad CFX software. Columns: transcript levels, error bars: standard error of the mean. (C) Summary of differentially expressed genes, downregulated or upregulated by depletion of ZNF217 and bound by ZNF217, ERα, or both ZNF217 and ERα.

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